Hysteresis multicycles in nanomagnet arrays

We predict two new physical effects in arrays of single-domain nanomagnets by performing simulations using a realistic model Hamiltonian and physical parameters. First, we find hysteretic multicycles for such nanomagnets. The simulation uses continuous spin dynamics through the Landau-Lifshitz-Gilbert (LLG) equation. In some regions of parameter space, the probability of finding a multicycle is as high as ~0.6. We find that systems with larger and more anisotropic nanomagnets tend to display more multicycles. This result demonstrates the importance of disorder and frustration for multicycle behavior. We also show that there is a fundamental difference between the more realistic vector LLG equation and scalar models of hysteresis, such as Ising models. In the latter case, spin and external field inversion symmetry is obeyed but in the former it is destroyed by the dynamics, with important experimental implications.Comment: 7 pages, 2 figure

Protein mechanical unfolding: importance of non-native interactions

Mechanical unfolding of the fourth domain of Distyostelium discoideum filamin (DDFLN4) was studied by all-atom molecular dynamics simulations, using the GROMOS96 force field 43a1 and the simple point charge explicit water solvent. Our study reveals an important role of non-native interactions in the unfolding process. Namely, the existence of a peak centered at the end-to-end extension 22 nm in the force-extension curve, is associated with breaking of non-native hydrogen bonds. Such a peak has been observed in experiments but not in Go models, where non-native interactions are neglected. We predict that an additional peak occurs at 2 nm using not only GROMOS96 force field 43a1 but also Amber 94 and OPLS force fields. This result would stimulate further experimental studies on elastic properties of DDFLN4.Comment: 27 pages, 15 figure

Loss of α-Synuclein Does Not Affect Mitochondrial Bioenergetics in Rodent Neurons.

Increased α-synuclein (αsyn) and mitochondrial dysfunction play central roles in the pathogenesis of Parkinson's disease (PD), and lowering αsyn is under intensive investigation as a therapeutic strategy for PD. Increased αsyn levels disrupt mitochondria and impair respiration, while reduced αsyn protects against mitochondrial toxins, suggesting that interactions between αsyn and mitochondria influences the pathologic and physiologic functions of αsyn. However, we do not know if αsyn affects normal mitochondrial function or if lowering αsyn levels impacts bioenergetic function, especially at the nerve terminal where αsyn is enriched. To determine if αsyn is required for normal mitochondrial function in neurons, we comprehensively evaluated how lowering αsyn affects mitochondrial function. We found that αsyn knockout (KO) does not affect the respiration of cultured hippocampal neurons or cortical and dopaminergic synaptosomes, and that neither loss of αsyn nor all three (α, β and γ) syn isoforms decreased mitochondria-derived ATP levels at the synapse. Similarly, neither αsyn KO nor knockdown altered the capacity of synaptic mitochondria to meet the energy requirements of synaptic vesicle cycling or influenced the localization of mitochondria to dopamine (DA) synapses in vivo. Finally, αsyn KO did not affect overall energy metabolism in mice assessed with a Comprehensive Lab Animal Monitoring System. These studies suggest either that αsyn has little or no significant physiological effect on mitochondrial bioenergetic function, or that any such functions are fully compensated for when lost. These results implicate that αsyn levels can be reduced in neurons without impairing (or improving) mitochondrial bioenergetics or distribution

Design, simulation, and characterization of a radial opposed migration ion and aerosol classifier (ROMIAC)

We present the design, simulation, and characterization of the radial opposed migration ion and aerosol classifier (ROMIAC), a compact differential electrical mobility classifier. We evaluate the performance of the ROMIAC using a combination of finite element modeling and experimental validation of two nearly identical instruments using tetra-alkyl ammonium halide mass standards and sodium chloride particles. Mobility and efficiency calibrations were performed over a wide range of particle diameters and flow rates to characterize ROMIAC performance under the range of anticipated operating conditions. The ROMIAC performs as designed, though performance deviates from that predicted using simplistic models of the instrument. The underlying causes of this non-ideal behavior are found through finite element simulations that predict the performance of the ROMIAC with greater accuracy than the simplistic models. It is concluded that analytical performance models based on idealized geometries, flows, and fields should not be relied on to make accurate a priori predictions about instrumental behavior if the actual geometry or fields deviate from the ideal assumptions. However, if such deviations are accurately captured, finite element simulations have the potential to predict instrumental performance. The present prototype of the ROMIAC maintains its resolution over nearly three orders of magnitude in particle mobility, obtaining sub-20 nm particle size distributions in a compact package with relatively low flow rate operation requirements

Nonlinear AC resistivity in s-wave and d-wave disordered granular superconductors

We model s-wave and d-wave disordered granular superconductors with a three-dimensional lattice of randomly distributed Josephson junctions with finite self-inductance. The nonlinear ac resistivity of these systems was calculated using Langevin dynamical equations. The current amplitude dependence of the nonlinear resistivity at the peak position is found to be a power law characterized by exponent $\alpha$. The later is not universal but depends on the self-inductance and current regimes. In the weak current regime $\alpha$ is independent of the self-inductance and equal to 0.5 or both of s- and d-wave materials. In the strong current regime this exponent depends on the screening. We find $\alpha \approx 1$ for some interval of inductance which agrees with the experimental finding for d-wave ceramic superconductors.Comment: 4 pages, 5 figures, to appear in Phys. Rev. Let

GEAR: A GPU-Centric Experience Replay System for Large Reinforcement Learning Models

This paper introduces a distributed, GPU-centric experience replay system, GEAR, designed to perform scalable reinforcement learning (RL) with large sequence models (such as transformers). With such models, existing systems such as Reverb face considerable bottlenecks in memory, computation, and communication. GEAR, however, optimizes memory efficiency by enabling the memory resources on GPU servers (including host memory and device memory) to manage trajectory data. Furthermore, it facilitates decentralized GPU devices to expedite various trajectory selection strategies, circumventing computational bottlenecks. GEAR is equipped with GPU kernels capable of collecting trajectories using zero-copy access to host memory, along with remote-directed-memory access over InfiniBand, improving communication efficiency. Cluster experiments have shown that GEAR can achieve performance levels up to 6× greater than Reverb when training state-of-the-art large RL models. GEAR is open-sourced at https://github.com/bigrl-team/gear

Finite size effects on thermal denaturation of globular proteins

Finite size effects on the cooperative thermal denaturation of proteins are considered. A dimensionless measure of cooperativity, Omega, scales as N^zeta, where N is the number of amino acids. Surprisingly, we find that zeta is universal with zeta = 1 + gamma, where the exponent gamma characterizes the divergence of the susceptibility for a self-avoiding walk. Our lattice model simulations and experimental data are consistent with the theory. Our finding rationalizes the marginal stability of proteins and substantiates the earlier predictions that the efficient folding of two-state proteins requires the folding transition temperature to be close to the collapse temperature.Comment: 3 figures. Physical Review Letters (in press