Path integral Monte Carlo simulations of silicates

We investigate the thermal expansion of crystalline SiO$_2$ in the $\beta$-- cristobalite and the $\beta$-quartz structure with path integral Monte Carlo (PIMC) techniques. This simulation method allows to treat low-temperature quantum effects properly. At temperatures below the Debye temperature, thermal properties obtained with PIMC agree better with experimental results than those obtained with classical Monte Carlo methods.Comment: 27 pages, 10 figures, Phys. Rev. B (in press

Sensing DNA through DNA Charge Transport

DNA charge transport chemistry involves the migration of charge over long molecular distances through the aromatic base pair stack within the DNA helix. This migration depends upon the intimate coupling of bases stacked one with another, and hence any perturbation in that stacking, through base modifications or protein binding, can be sensed electrically. In this review, we describe the many ways DNA charge transport chemistry has been utilized to sense changes in DNA, including the presence of lesions, mismatches, DNA-binding proteins, protein activity, and even reactions under weak magnetic fields. Charge transport chemistry is remarkable in its ability to sense the integrity of DNA

The Oxidation State of [4Fe4S] Clusters Modulates the DNA-Binding Affinity of DNA Repair Proteins

A central question important to understanding DNA repair is how certain proteins are able to search for, detect, and fix DNA damage on a biologically relevant time scale. A feature of many base excision repair proteins is that they contain [4Fe4S] clusters that may aid their search for lesions. In this paper, we establish the importance of the oxidation state of the redox-active [4Fe4S] cluster in the DNA damage detection process. We utilize DNA-modified electrodes to generate repair proteins with [4Fe4S] clusters in the 2+ and 3+ states by bulk electrolysis under an O_2-free atmosphere. Anaerobic microscale thermophoresis results indicate that proteins carrying [4Fe4S]^(3+) clusters bind to DNA 550 times more tightly than those with [4Fe4S]^(2+) clusters. The measured increase in DNA-binding affinity matches the calculated affinity change associated with the redox potential shift observed for [4Fe4S] cluster proteins upon binding to DNA. We further devise an electrostatic model that shows this change in DNA-binding affinity of these proteins can be fully explained by the differences in electrostatic interactions between DNA and the [4Fe4S] cluster in the reduced versus oxidized state. We then utilize atomic force microscopy (AFM) to demonstrate that the redox state of the [4Fe4S] clusters regulates the ability of two DNA repair proteins, Endonuclease III and DinG, to bind preferentially to DNA duplexes containing a single site of DNA damage (here a base mismatch) which inhibits DNA charge transport. Together, these results show that the reduction and oxidation of [4Fe4S] clusters through DNA-mediated charge transport facilitates long-range signaling between [4Fe4S] repair proteins. The redox-modulated change in DNA-binding affinity regulates the ability of [4Fe4S] repair proteins to collaborate in the lesion detection process

Frequency-Dependent Squeezing for Advanced LIGO

The first detection of gravitational waves by the Laser Interferometer Gravitational-wave Observatory (LIGO) in 2015 launched the era of gravitational wave astronomy. The quest for gravitational wave signals from objects that are fainter or farther away impels technological advances to realize ever more sensitive detectors. Since 2019, one advanced technique, the injection of squeezed states of light is being used to improve the shot noise limit to the sensitivity of the Advanced LIGO detectors, at frequencies above $\sim 50$ Hz. Below this frequency, quantum back action, in the form of radiation pressure induced motion of the mirrors, degrades the sensitivity. To simultaneously reduce shot noise at high frequencies and quantum radiation pressure noise at low frequencies requires a quantum noise filter cavity with low optical losses to rotate the squeezed quadrature as a function of frequency. We report on the observation of frequency-dependent squeezed quadrature rotation with rotation frequency of 30Hz, using a 16m long filter cavity. A novel control scheme is developed for this frequency-dependent squeezed vacuum source, and the results presented here demonstrate that a low-loss filter cavity can achieve the squeezed quadrature rotation necessary for the next planned upgrade to Advanced LIGO, known as "A+."Comment: 6 pages, 2 figures, to be published in Phys. Rev. Let

How Many Muscles? Optimal Muscles Set Search for Optimizing Myocontrol Performance

In myo-control, for computational and setup constraints, the measurement of a high number of muscles is not always possible: the choice of the muscle set to use in a myo-control strategy depends on the desired application scope and a search for a reduced muscle set, tailored to the application, has never been performed. The identification of such set would involve finding the minimum set of muscles whose difference in terms of intention detection performance is not statistically significant when compared to the original set. Also, given the intrinsic sensitivity of muscle synergies to variations of EMG signals matrix, the reduced set should not alter synergies that come from the initial input, since they provide physiological information on motor coordination. The advantages of such reduced set, in a rehabilitation context, would be the reduction of the inputs processing time, the reduction of the setup bulk and a higher sensitivity to synergy changes after training, which can eventually lead to modifications of the ongoing therapy. In this work, the existence of a minimum muscle set, called optimal set, for an upper-limb myoelectric application, that preserves performance of motor activity prediction and the physiological meaning of synergies, has been investigated. Analyzing isometric contractions during planar reaching tasks, two types of optimal muscle sets were examined: a subject-specific one and a global one. The former relies on the subject-specific movement strategy, the latter is composed by the most recurrent muscles among subjects specific optimal sets and shared by all the subjects. Results confirmed that the muscle set can be reduced to achieve comparable hand force estimation performances. Moreover, two types of muscle synergies namely “Pose-Shared” (extracted from a single multi-arm-poses dataset) and “Pose-Related” (clustering pose-specific synergies), extracted from the global optimal muscle set, have shown a significant similarity with full-set related ones meaning a high consistency of the motor primitives. Pearson correlation coefficients assessed the similarity of each synergy. The discovering of dominant muscles by means of the optimization of both muscle set size and force estimation error may reveal a clue on the link between synergistic patterns and the force task

Effective Distance for DNA-Mediated Charge Transport between Repair Proteins

The stacked aromatic base pairs within the DNA double helix facilitate charge transport down its length in the absence of lesions, mismatches, and other stacking perturbations. DNA repair proteins containing [4Fe4S] clusters can take advantage of DNA charge transport (CT) chemistry to scan the genome for mistakes more efficiently. Here we examine the effective length over which charge can be transported along DNA between these repair proteins. We define the effective CT distance as the length of DNA within which two proteins are able to influence their ensemble affinity to the DNA duplex via CT. Endonuclease III, a DNA repair glycosylase containing a [4Fe4S] cluster, was incubated with DNA duplexes of different lengths (1.5–9 kb), and atomic force microscopy was used to quantify the binding of proteins to these duplexes to determine how the relative protein affinity changes with increasing DNA length. A sharp change in binding slope is observed at 3509 base pairs, or about 1.2 μm, that supports the existence of two regimes for protein binding, one within the range for DNA CT, one outside of the range for CT; DNA CT between the redox proteins bound to DNA effectively decreases the ensemble binding affinity of oxidized and reduced proteins to DNA. Utilizing an Endonuclease III mutant Y82A, which is defective in carrying out DNA CT, shows only one regime for protein binding. Decreasing the temperature to 4 °C or including metallointercalators on the duplex, both of which should enhance base stacking and decrease DNA floppiness, leads to extending the effective length for DNA charge transport to ∼5300 bp or 1.8 μm. These results thus support DNA charge transport between repair proteins over kilobase distances. The results furthermore highlight the ability of DNA repair proteins to search the genome quickly and efficiently using DNA charge transport chemistry

Introduction of electric vehicle charging stations to university campuses : A case study for the university of Georgia from 2014 to 2017

Electric vehicles (EVs) are becoming increasingly popular in the United States of America (USA). EVs attract buyers with benefits including energy efficiency and environmental friendliness. As EV usage grows, more public spaces are installing EV charging stations. This paper presents a comprehensive analysis of EV charging station usage at the University of Georgia (UGA) in Athens, Georgia. Three ChargePoint EV charging stations at UGA were used to collect data about each of 3204 charging events that occurred from 10 April 2014 to 20 June 2017. The charging event data included start date, start time, length of parking time, length of charging time, amount of energy delivered, and the postal code entered by the user during ChargePoint account registration. Analytical methods were proposed to obtain information about EV charging behavior, charging station occupancy, and geolocation of charging station users. The methodology presented here was time- and cost-effective, as well as scalable to other organizations that own charging stations. Because this study took place at a university, the results presented here can be used as a reference for EV charging station usage in other college towns in the USA that do not have EV charging stations but are planning to develop EV infrastructure