arXiv subjects

Alvaro Sanchez

Publications and source records attributed to Alvaro Sanchez.

At least 19 recordsLinked to original sources

arXiv2025

Humanity's Last Exam

Benchmarks are important tools for tracking the rapid advancements in large language model (LLM) capabilities. However, benchmarks are not keeping pace in difficulty: LLMs now achieve over 90\% accuracy on popular benchmarks like MMLU, limiting informed measurement of state-of-the-art LLM capabilities. In response, we introduce Humanity's Last Exam (HLE), a multi-modal benchmark at the frontier of human knowledge, designed to be the final closed-ended academic benchmark of its kind with broad subject coverage. HLE consists of 2,500 questions across dozens of subjects, including mathematics, humanities, and the natural sciences. HLE is developed globally by subject-matter experts and consists of multiple-choice and short-answer questions suitable for automated grading. Each question has a known solution that is unambiguous and easily verifiable, but cannot be quickly answered via internet retrieval. State-of-the-art LLMs demonstrate low accuracy and calibration on HLE, highlighting a significant gap between current LLM capabilities and the expert human frontier on closed-ended academic questions. To inform research and policymaking upon a clear understanding of model capabilities, we publicly release HLE at https://lastexam.ai.

cs.LG↗

arXiv2022

Complete and Robust Magnetic Field Confinement by Superconductors in Fusion Magnets

The fusion created by magnetically confined plasma is a promising clean and essentially unlimited future energy source. However, net energy generation has not been yet demonstrated in fusion experiments. Some of the main problems hindering controlled fusion are the imperfect magnetic confinement and the associated plasma instabilities. Here, we theoretically demonstrate how to create a fully confined magnetic field with the precise three-dimensional shape required by fusion theory, using a bulk superconducting toroid with a toroidal cavity. The combination of the properties of superconductors with the toroidal topology makes the vacuum field in the cavity volume consisting of nested flux surfaces, a condition for optimum plasma confinement. The coils creating the field, embedded in the superconducting bulk, can be chosen with very simple shapes, in contrast with the cumbersome arrangements in current experiments, and can be spared from the large magnetic forces between them. Because the field shape in the cavity is given by the boundary conditions in the superconductor surface, the system will always tend to maintain the optimum field distribution in response to instabilities or turbulence in the plasma. This field shape is preserved even when holes are drilled in the superconductor to access the plasma region from the exterior. We demonstrate how a fully-confined magnetic field with the three-dimensional spatial distribution required in two of the most advanced stellarators, Large Helical Device and Wendelstein 7-X, can be exactly generated, using simple round coils as magnetic sources. We argue that state-of-the-art high-temperature superconductors already have the necessary properties to be employed to construct the bulk superconducting toroid. The present strategy can lead to optimized robust magnetic confinement and largely simplified configurations in future fusion experiments.

physics.plasm-ph↗

arXiv2022

Global epistasis on fitness landscapes

Epistatic interactions between mutations add substantial complexity to adaptive landscapes, and are often thought of as detrimental to our ability to predict evolution. Yet, patterns of global epistasis, in which the fitness effect of a mutation is well-predicted by the fitness of its genetic background, may actually be of help in our efforts to reconstruct fitness landscapes and infer adaptive trajectories. Microscopic interactions between mutations, or inherent nonlinearities in the fitness landscape, may cause global epistasis patterns to emerge. In this brief review, we provide a succinct overview of recent work about global epistasis, with an emphasis on building intuition about why it is often observed. To this end, we reconcile simple geometric reasoning with recent mathematical analyses, using these to explain why different mutations in an empirical landscape may exhibit different global epistasis patterns - ranging from diminishing to increasing returns. Finally, we highlight open questions and research directions.

q-bio.PE↗

arXiv2021

Shaping Magnetic Fields with Zero-Magnetic-Permeability Media

Some of the most important technological challenges of today's society, such as fusion reactors for future clean unlimited energy or the next generation of medical imaging techniques, require precise spatial shapes of strong magnetic fields. Achieving these high fields is currently hindered by limitations such as large forces damaging the wires in coils or the saturation of ferromagnets at high fields. Here we demonstrate a novel paradigm for creating magnetic landscapes. By enclosing magnetic sources within zero-magnetic-permeability (ZMP) media, a set of novel properties is unveiled. The magnetic field shape directly results from the contour of the outer surface of the ZMP enclosure, which allows the realization of basically any imaginable field landscape. Also, currents embedded in ZMP media can be fully magnetically isolated, which eliminates the forces in the wires, one of the main factors that currently impedes achieving very high magnetic fields. We confirm these properties, rooted in fundamental laws of electromagnetism, by numerical simulations and by proof-of-principle experiments using conventional high-temperature superconductors as ZMP materials, which showcase the practical applicability of our ideas. The freedom in the design of magnetic fields provided by ZMP media enables to concentrate and homogenize magnetic fields with unprecedented precision, as needed in medical imaging techniques and particle-physics experiments, and to realize devices like perfect electromagnetic absorbers of mechanical vibrations.

physics.app-ph↗

arXiv2021

Mechanical frequency control in inductively coupled electromechanical systems

Nano-electromechanical systems implement the opto-mechanical interaction combining electromagnetic circuits and mechanical elements. We investigate an inductively coupled nano-electromechanical system, where a superconducting quantum interference device (SQUID) realizes the coupling. We show that the resonance frequency of the mechanically compliant string embedded into the SQUID loop can be controlled in two different ways: (i) the bias magnetic flux applied perpendicular to the SQUID loop, (ii) the magnitude of the in-plane bias magnetic field contributing to the nano-electromechanical coupling. These findings are quantitatively explained by the inductive interaction contributing to the effective spring constant of the mechanical resonator. In addition, we observe a residual field dependent shift of the mechanical resonance frequency, which we attribute to the finite flux pinning of vortices trapped in the magnetic field biased nanostring.

quant-ph↗

arXiv2020

Levitation of superconducting micro-rings for quantum magnetomechanics

Levitation of superconductors is becoming an important building block in quantum technologies, particularly in the rising field of magnetomechanics. In most of the theoretical proposals and experiments, solid geometries such as spheres are considered for the levitator. Here we demonstrate that replacing them by superconducting rings brings two important advantages: Firstly, the forces acting on the ring remain comparable to those expected for solid objects, while the mass of the superconductor is greatly reduced. In turn, this reduction increases the achievable trap frequency. Secondly, the flux trapped in the ring by in-field cooling yields an additional degree of control for the system. We construct a general theoretical framework with which we obtain analytical formulations for a superconducting ring levitating in an anti-Helmholtz quadrupole field and a dipole field, for both zero-field and in-field cooling. The positions and the trapping frequencies of the levitated rings are analytically found as a function of the parameters of the system and the field applied during the cooling process. Unlike what is commonly observed in bulk superconductors, lateral and rotational stability are not granted for this idealized geometry. We therefore discuss the requirements for simple superconducting structures to achieve stability in all degrees of freedom.

cond-mat.supr-con↗

arXiv2020

The homology of the groupoid of the self-similar dihedral group

We give an example of a locally compact effective Hausdorff, minimal ample groupoid such that its rational homology differs from the $K$-theory of its reduced groupoid $C^*$-algebra. Moreover, we prove that such example satisfies Matui's AH-conjecture.

math.OA↗

arXiv2020

Computation Of Microbial Ecosystems in Time and Space (COMETS): An open source collaborative platform for modeling ecosystems metabolism

Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are also emerging as a valuable avenue for predicting, understanding and designing microbial communities. COMETS (Computation Of Microbial Ecosystems in Time and Space) was initially developed as an extension of dynamic flux balance analysis, which incorporates cellular and molecular diffusion, enabling simulations of multiple microbial species in spatially structured environments. Here we describe how to best use and apply the most recent version of this platform, COMETS 2, which incorporates a more accurate biophysical model of microbial biomass expansion upon growth, as well as several new biological simulation modules, including evolutionary dynamics and extracellular enzyme activity. COMETS 2 provides user-friendly Python and MATLAB interfaces compatible with the well-established COBRA models and methods, and comprehensive documentation and tutorials, facilitating the use of COMETS for researchers at all levels of expertise with metabolic simulations. This protocol provides a detailed guideline for installing, testing and applying COMETS 2 to different scenarios, with broad applicability to microbial communities across biomes and scales.

q-bio.QM↗

arXiv2019

Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities

A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences between the microbes and their chemical environment through the consumption and production of metabolites. By analyzing a generalized consumer resource model that explicitly includes cross-feeding, stochastic colonization, and thermodynamics, we show that complex microbial communities generically exhibit a transition as a function of available energy fluxes from a "resource-limited" regime where community structure and stability is shaped by energetic and metabolic considerations to a diverse regime where the dominant force shaping microbial communities is the overlap between species' consumption preferences. These two regimes have distinct species abundance patterns, different functional profiles, and respond differently to environmental perturbations. Our model reproduces large-scale ecological patterns observed across multiple experimental settings such as nestedness and differential beta diversity patterns along energy gradients. We discuss the experimental implications of our results and possible connections with disorder-induced phase transitions in statistical physics.

physics.bio-ph↗

arXiv2018

Accelerating, guiding, and compressing skyrmions by defect rails

Magnetic skyrmions are promising candidates as information carriers in spintronic devices. The transport of individual skyrmions in a fast and controlled way is a key issue in this field. Here we introduce a novel platform for accelerating, guiding and compressing skyrmions along predefined paths. The guiding mechanism is based on two parallel defect-lines (rails), one attractive and the other repulsive. Numerical simulations, using parameters from state-of-the-art experiments, show that the speed of the skyrmions along the rails is increased up to a factor of ten with respect to the non-defect case whereas the distance between rails can be as small as the initial radius of the skyrmions. In this way, the flux of information that can be coded and transported with magnetic skyrmions could be significantly increased.

cond-mat.mes-hall↗

arXiv2018

Magnetic illusion: transforming a magnetic object into another object by negative permeability

We theoretically predict and experimentally verify the illusion of transforming the magnetic signature of a 3D object into that of another arbitrary object. This is done by employing negative-permeability materials, which we demonstrate that can be emulated by tailored sets of currents. The experimental transformation of the magnetic response of a ferromagnet into that of its antagonistic material, a superconductor, is presented to confirm the theory. The emulation of negative-permeability materials by currents provides a new pathway for designing devices for controlling magnetic fields in unprecedented ways.

cond-mat.mtrl-sci↗

arXiv2018

Negative permeability in magnetostatics and its experimental demonstration

The control of magnetic fields, essential for our science and technology, is currently achieved by magnetic materials with positive permeability, including ferromagnetic, paramagnetic, and diamagnetic types. Here we introduce materials with negative static permeability as a new paradigm for manipulating magnetic fields. As a first step, we extend the solutions of Maxwell magnetostatic equations to include negative-permeability values. The understanding of these new solutions allow us to devise a negative-permeability material as a suitably tailored set of currents arranged in space, overcoming the fact that passive materials with negative permeability do no exist in magnetostatics. We confirm the theory by experimentally creating a spherical shell that emulates a negative-permeability material in a uniform magnetic field. Our results open new possibilities for creating and manipulating magnetic fields, which can be useful for practical applications.

cond-mat.mtrl-sci↗

arXiv2014

Long-Distance Transfer and Routing of Static Magnetic Fields

We show how the static magnetic field of a finite source can be transferred and routed to arbitrary long distances. This is achieved by using transformation optics, which results in a device made of a material with a highly anisotropic magnetic permeability. We show that a simplified version of the device, made by a superconducting-ferromagnet hybrid, also leads to an excellent transfer of the magnetic field. The latter is demonstrated with a proof-of-principle experiment where a ferromagnet tube coated with a superconductor improves the transfer of static magnetic fields with respect to conventional methods by a 400\% factor over distances of 14cm.

cond-mat.supr-con↗

arXiv2014

Imprinting skyrmions in thin films by ferromagnetic and superconducting templates

Magnetic skyrmions are promising candidates as information carriers in a new generation of memories. How to generate and stabilize skyrmions is essential for their successful application to technology. Here we theoretically demonstrate that arrays of skyrmions can be imprinted in ultrathin ferromagnetic films in large numbers by bringing a magnetic nanostructured template close to the film. Two kind of templates, allowed by present-day nanotechnologies, are studied: arrays of ferromagnetic nanorods and superconducting vortices. Skyrmions are generated when exposing magnetic films to the template fields for short times and remain stable after removing the template.

cond-mat.mtrl-sci↗

arXiv2014

Deciphering transcriptional dynamics in vivo by counting nascent RNA molecules

Transcription of genes is the focus of most forms of regulation of gene expression. Even though careful biochemical experimentation has revealed the molecular mechanisms of transcription initiation for a number of different promoters in vitro, the dynamics of this process in cells is still poorly understood. One approach has been to measure the transcriptional output (fluorescently labeled messenger RNAs or proteins) from single cells in a genetically identical population, which could then be compared to predictions from models that incorporate different molecular mechanisms of transcription initiation. However, this approach suffers from the problem, that processes downstream from transcription can affect the measured output and therefore mask the signature of stochastic transcription initiation on the cell-to-cell variability of the transcriptional outputs. Here we show theoretically that measurements of the cell-to-cell variability in the number of nascent RNAs provide a more direct test of the mechanism of transcription initiation. We derive exact expressions for the first two moments of the distribution of nascent RNA molecules and apply our theory to published data for a collection of constitutively expressed yeast genes. We find that the measured nascent RNA distributions are inconsistent with transcription initiation proceeding via one rate-limiting step, which has been generally inferred from measurements of cytoplasmic messenger RNA. Instead, we propose a two-step mechanism of initiation, which is consistent with the available data. These findings for the yeast promoters highlight the utility of our theory for deciphering transcriptional dynamics in vivo from experiments that count nascent RNA molecules in single cells.

q-bio.MN↗

arXiv2013

Experimental realization of magnetic energy concentration and transmission at a distance by metamaterials

Controlling electromagnetic energy is essential for an efficient and sustainable society. A key requirement is concentrating magnetic energy in a desired volume of space in order to either extract the energy to produce work or store it. Metamaterials have opened new possibilities for controlling electromagnetic energy. Recently, a superconductor-ferromagnetic metamaterial that allows unprecedented concentration and amplification of magnetic energy, and also its transmission at distance through free space, has been devised theoretically. Here we design and build an actual version of the superconductor-ferromagnetic metamaterial and experimentally confirm these properties. We show that also a ferromagnetic metamaterial, without superconducting parts, can achieve concentration and transmission of energy with only a slight decrease in the performance. Transmission of magnetic energy at a distance by magnetic metamaterials may provide new ways of enhancing wireless power transmission, where efficiency depends critically on the magnetic coupling strength between source and receiver.

cond-mat.supr-con↗

arXiv2013

Dynamics of a producer-parasite ecosystem on the brink of collapse

Ecosystems can undergo sudden shifts to undesirable states, but recent studies with simple single species ecosystems have demonstrated that advance warning can be provided by the slowing down of population dynamics near a tipping point. However, it is not clear how this effect of critical slowing down will manifest in ecosystems with strong interactions between their components. Here we probe the dynamics of an experimental producer parasite ecosystem as it approaches a catastrophic collapse. Surprisingly, the producer population grows in size as the environment deteriorates, highlighting that population size can be a misleading measure of ecosystem stability. By analyzing the oscillatory producer parasite dynamics for over ~100 generations in multiple environmental conditions, we found that the collective ecosystem dynamics slows down as the tipping point is approached. Analysis of the coupled dynamics of interacting populations may therefore be necessary to provide advance warning of collapse in complex communities.

q-bio.PE↗

arXiv2013

Feedback between population and evolutionary dynamics determines the fate of social microbial populations

The evolutionary spread of cheater strategies can destabilize populations engaging in cooperative behaviors, thus demonstrating that evolutionary changes can have profound implications for populations dynamics. At the same time, the relative fitness of cooperative traits often depends upon population density, thus leading to the potential for bidirectional coupling between population density and the evolution of a cooperative trait. Despite the potential importance of these eco evolutionary feedback loops, they have not yet been demonstrated experimentally in social species and their ecological implications are poorly understood. Here, we demonstrate the presence of a strong feedback loop between population dynamics and the evolutionary dynamics of a social microbial gene, SUC2, in laboratory yeast populations whose cooperative growth is mediated by the SUC2 gene. We directly visualize eco evolutionary trajectories of hundreds of populations over fifty generations, allowing us to characterize the phase space describing the interplay of evolution and ecology in this system. Small populations collapse despite continual evolution towards increased cooperative allele frequencies; large populations with a sufficient number of cooperators spiral to a stable state of coexistence between cooperator and cheater strategies. The presence of cheaters does not significantly affect the equilibrium population density, but it does reduce the resilience of the population as well as its ability to adapt to a rapidly deteriorating environment. Our results demonstrate the potential ecological importance of coupling between evolutionary dynamics and the population dynamics of cooperatively growing organisms, particularly in microbes.

q-bio.PE↗