RAM-Efficient External Memory Sorting

In recent years a large number of problems have been considered in external memory models of computation, where the complexity measure is the number of blocks of data that are moved between slow external memory and fast internal memory (also called I/Os). In practice, however, internal memory time often dominates the total running time once I/O-efficiency has been obtained. In this paper we study algorithms for fundamental problems that are simultaneously I/O-efficient and internal memory efficient in the RAM model of computation.Comment: To appear in Proceedings of ISAAC 2013, getting the Best Paper Awar

Stationary structure of relativistic superfluid neutron stars

We describe recent progress in the numerical study of the structure of rapidly rotating superfluid neutron star models in full general relativity. The superfluid neutron star is described by a model of two interpenetrating and interacting fluids, one representing the superfluid neutrons and the second consisting of the remaining charged particles (protons, electrons, muons). We consider general stationary configurations where the two fluids can have different rotation rates around a common rotation axis. The previously discovered existence of configurations with one fluid in a prolate shape is confirmed.Comment: 5 pages, 2 figures. Conference proceedings for the 26th Spanish Relativity Meeting (ERE 2002), Menorca, Spain, 22-24 Sept. 200

Subdiffusion in Membrane Permeation of Small Molecules

Citation: Chipot, C. and Comer, J. Subdiffusion in Membrane Permeation of Small Molecules. Sci. Rep. 6, 35913; doi: 10.1038/srep35913 (2016).Within the solubility–diffusion model of passive membrane permeation of small molecules, translocation of the permeant across the biological membrane is traditionally assumed to obey the Smoluchowski diffusion equation, which is germane for classical diffusion on an inhomogeneous free-energy and diffusivity landscape. This equation, however, cannot accommodate subdiffusive regimes, which have long been recognized in lipid bilayer dynamics, notably in the lateral diffusion of individual lipids. Through extensive biased and unbiased molecular dynamics simulations, we show that one-dimensional translocation of methanol across a pure lipid membrane remains subdiffusive on timescales approaching typical permeation times. Analysis of permeant motion within the lipid bilayer reveals that, in the absence of a net force, the mean squared displacement depends on time as t0.7, in stark contrast with the conventional model, which assumes a strictly linear dependence. We further show that an alternate model using a fractional-derivative generalization of the Smoluchowski equation provides a rigorous framework for describing the motion of the permeant molecule on the pico- to nanosecond timescale. The observed subdiffusive behavior appears to emerge from a crossover between small-scale rattling of the permeant around its present position in the membrane and larger-scale displacements precipitated by the formation of transient voids

A Relativistic Mean Field Model for Entrainment in General Relativistic Superfluid Neutron Stars

General relativistic superfluid neutron stars have a significantly more intricate dynamics than their ordinary fluid counterparts. Superfluidity allows different superfluid (and superconducting) species of particles to have independent fluid flows, a consequence of which is that the fluid equations of motion contain as many fluid element velocities as superfluid species. Whenever the particles of one superfluid interact with those of another, the momentum of each superfluid will be a linear combination of both superfluid velocities. This leads to the so-called entrainment effect whereby the motion of one superfluid will induce a momentum in the other superfluid. We have constructed a fully relativistic model for entrainment between superfluid neutrons and superconducting protons using a relativistic $\sigma - \omega$ mean field model for the nucleons and their interactions. In this context there are two notions of ``relativistic'': relativistic motion of the individual nucleons with respect to a local region of the star (i.e. a fluid element containing, say, an Avogadro's number of particles), and the motion of fluid elements with respect to the rest of the star. While it is the case that the fluid elements will typically maintain average speeds at a fraction of that of light, the supranuclear densities in the core of a neutron star can make the nucleons themselves have quite high average speeds within each fluid element. The formalism is applied to the problem of slowly-rotating superfluid neutron star configurations, a distinguishing characteristic being that the neutrons can rotate at a rate different from that of the protons.Comment: 16 pages, 5 figures, submitted to PR

"What do you Mean I Cannot Consent For My Grandmother's Medical Procedure?": Key Issues With State Default Surrogate Decision Making Laws

When a patient is unable to make medical decisions, a health care surrogate must be designated to make decisions on the patient's behalf. Studies show that fewer than 20% of patients have completed health care representative forms to legally designate a surrogate. Without a prior designation, surrogates are determined via state statute. Currently, there is no up-to-date comprehensive evaluation of state surrogate legislation. A survey of state legislative codes was conducted to determine: 1) whether the state has a default surrogate statute; 2) who is included as an acceptable legal surrogate; and 3) whether there is a hierarchy to determine a final decision-maker. Currently, 36 states have enacted some form of surrogate statute. There is little consistency between states regarding who may serve as a surrogate decision- maker. The key challenges with state laws include: 1) a narrow list of persons who qualify as allowable legal surrogates; and 2) a lack of a hierarchy to determine a final decision-maker. The results of this survey show that state surrogate decision making laws have many flaws which could affect patient care. The narrow construction of state laws can leave patients in situations where they either have no qualified surrogate under the law, or where they have multiple surrogates with competing interests who may be unable to reach consensus on the patient's medical care. State laws need to be changed so that they accurately reflect the realities of clinical practice and expanded to allow a broader spectrum of potential surrogates

Slowly Rotating General Relativistic Superfluid Neutron Stars with Relativistic Entrainment

Neutron stars that are cold enough should have two or more superfluids/supercondutors in their inner crusts and cores. The implication of superfluidity/superconductivity for equilibrium and dynamical neutron star states is that each individual particle species that forms a condensate must have its own, independent number density current and equation of motion that determines that current. An important consequence of the quasiparticle nature of each condensate is the so-called entrainment effect, i.e. the momentum of a condensate is a linear combination of its own current and those of the other condensates. We present here the first fully relativistic modelling of slowly rotating superfluid neutron stars with entrainment that is accurate to the second-order in the rotation rates. The stars consist of superfluid neutrons, superconducting protons, and a highly degenerate, relativistic gas of electrons. We use a relativistic $\sigma$ - $\omega$ mean field model for the equation of state of the matter and the entrainment. We determine the effect of a relative rotation between the neutrons and protons on a star's total mass, shape, and Kepler, mass-shedding limit.Comment: 30 pages, 10 figures, uses ReVTeX

Determinants of Alanine Dipeptide Conformational Equilibria on Graphene and Hydroxylated Derivatives

Citation: Poblete, H., Miranda-Carvajal, I., & Comer, J. (2017). Determinants of Alanine Dipeptide Conformational Equilibria on Graphene and Hydroxylated Derivatives. The Journal of Physical Chemistry B. https://doi.org/10.1021/acs.jpcb.7b01130Understanding the interaction of carbon nanomaterials with proteins is essential for determining the potential effects of these materials on health and in the design of biotechnology based on them. Here we leverage explicit-solvent molecular simulation and multidimensional free-energy calculations to investigate how adsorption to carbon nanomaterial surfaces affects the conformational equilibrium of alanine dipeptide, a widely used model of protein backbone structure. We find that the two most favorable structures of alanine dipeptide on graphene (or large carbon nanotubes) correspond to the two amide linkages lying in the same plane, flat against the surface, rather than the nonplanar ?-helix-like and ?-sheet-like conformations that predominate in aqueous solution. On graphenic surfaces, the latter conformations are metastable and most often correspond to amide?? stacking of the N-terminal amide. The calculations highlight the key role of amide?? interactions in determining the conformational equilibrium. Lesser but significant contributions from hydrogen bonding to the high density interfacial water layer or to the hydroxy groups of hydroxylated graphene also define the most favorable conformations. This work should yield insight on the influence of carbon nanotubes, graphene, and their functionalized derivatives on protein structure

Collapse of a Circular Loop of Cosmic String

We study the collapse of a circular loop of cosmic string. The gravitational field of the string is treated using the weak field approximation. The gravitational radiation from the loop is evaluated numerically. The memtric of the loop near the point of collapse is found analytically.Comment: 15 page

Generation of scalar-tensor gravity effects in equilibrium state boson stars

Boson stars in zero-, one-, and two-node equilibrium states are modeled numerically within the framework of Scalar-Tensor Gravity. The complex scalar field is taken to be both massive and self-interacting. Configurations are formed in the case of a linear gravitational scalar coupling (the Brans-Dicke case) and a quadratic coupling which has been used previously in a cosmological context. The coupling parameters and asymptotic value for the gravitational scalar field are chosen so that the known observational constraints on Scalar-Tensor Gravity are satisfied. It is found that the constraints are so restrictive that the field equations of General Relativity and Scalar-Tensor gravity yield virtually identical solutions. We then use catastrophe theory to determine the dynamically stable configurations. It is found that the maximum mass allowed for a stable state in Scalar-Tensor gravity in the present cosmological era is essentially unchanged from that of General Relativity. We also construct boson star configurations appropriate to earlier cosmological eras and find that the maximum mass for stable states is smaller than that predicted by General Relativity, and the more so for earlier eras. However, our results also show that if the cosmological era is early enough then only states with positive binding energy can be constructed.Comment: 20 pages, RevTeX, 11 figures, to appear in Class. Quantum Grav., comments added, refs update