Using nonequilibrium fluctuation theorems to understand and correct errors in equilibrium and nonequilibrium discrete Langevin dynamics simulations

Common algorithms for computationally simulating Langevin dynamics must discretize the stochastic differential equations of motion. These resulting finite time step integrators necessarily have several practical issues in common: Microscopic reversibility is violated, the sampled stationary distribution differs from the desired equilibrium distribution, and the work accumulated in nonequilibrium simulations is not directly usable in estimators based on nonequilibrium work theorems. Here, we show that even with a time-independent Hamiltonian, finite time step Langevin integrators can be thought of as a driven, nonequilibrium physical process. Once an appropriate work-like quantity is defined -- here called the shadow work -- recently developed nonequilibrium fluctuation theorems can be used to measure or correct for the errors introduced by the use of finite time steps. In particular, we demonstrate that amending estimators based on nonequilibrium work theorems to include this shadow work removes the time step dependent error from estimates of free energies. We also quantify, for the first time, the magnitude of deviations between the sampled stationary distribution and the desired equilibrium distribution for equilibrium Langevin simulations of solvated systems of varying size. While these deviations can be large, they can be eliminated altogether by Metropolization or greatly diminished by small reductions in the time step. Through this connection with driven processes, further developments in nonequilibrium fluctuation theorems can provide additional analytical tools for dealing with errors in finite time step integrators.Comment: 11 pages, 4 figure

Teacher, Mentor, Friend, Leader

It is a rare person who through his own thoughts and efforts can truly be said to have changed this country, and the world, for the better. Fewer still do it with humility and grace. Frank E. A. Sander is one such transformative figure, a man who for nearly 40 years has nurtured the field of dispute resolution that today is credited as being one of the most significant shifts in American law. Inspired by his ideas and efforts, the resolution of legal problems is faster, more humane, more effective, and less costly for those in the United States and across the globe

Photochemical aerosol formation from α-pinene- and β-pinene

Aerosol formation from α-pinene and β-pinene was studied in a series of outdoor smog chamber experiments. Since a previous study focused on β-pinene (Pandis et al., 1991), more attention was given here to α-pinene. The initial hydrocarbon and NO_x concentrations ranged from 37 to 582 ppb and 31 to 380 ppb, respectively. The aerosol carbon yield, the fraction of the carbon initially present that is converted to aerosol, varied from 0 to 5.3% for α-pinene, depending on the initial hydrocarbon-to-NO_x ratio. Dual-bag experiments demonstrate that α-pinene is more rapidly photooxidized, and produces higher yields of both aerosol and ozone in a given period of time than β-pinene, although given sufficient time β-pinene can produce equivalent aerosol yields. Although aerosol formation solely from isoprene photooxidation was found in a previous study to be negligible under ambient conditions, the addition of isoprene to the α-pinene/NO_x system leads to an increased aerosol yield through the enhanced photochemical activity generated

Effects of current speed and turbidity on stationary light-trap catches of larval and juvenile fishes

Light traps are one of a number of different gears used to sample pelagic larval and juvenile fishes. In contrast to conventional towed nets, light traps primarily collect larger size classes, including settlement-size larvae (Choat et al., 1993; Hickford and Schiel, 1999 ; Hernandez and Shaw, 2003), and, therefore, have become important tools for discerning recruitment dynamics (Sponaugle and Cowen, 1996; Wilson, 2001). The relative ease with which multiple synoptic light trap samples can be taken means that larval distribution patterns can be mapped with greater spatial resolution (Doherty, 1987). Light traps are also useful for sampling shallow or structurally complex habitats where towed nets are ineffective or prohibited (Gregory and Powles, 1985; Brogan, 1994; Hernandez and Shaw, 2003)

Inhibition of the \u3cem\u3edapE\u3c/em\u3e-Encoded \u3cem\u3eN\u3c/em\u3e-Succinyl- ʟ, ʟ-diaminopimelic Acid Desuccinylase from \u3cem\u3eNeisseria meningitidis\u3c/em\u3e by ʟ-Captopril

Binding of the competitive inhibitor ʟ-captopril to the dapE-encoded N-succinyl-ʟ, ʟ-diaminopimelic acid desuccinylase from Neisseria meningitidis (NmDapE) was examined by kinetic, spectroscopic, and crystallographic methods. ʟ-Captopril, an angiotensin-converting enzyme (ACE) inhibitor, was previously shown to be a potent inhibitor of the DapE from Haemophilus influenzae (HiDapE) with an IC50 of 3.3 μM and a measured Ki of 1.8 μM and displayed a dose-responsive antibiotic activity toward Escherichia coli. ʟ-Captopril is also a competitive inhibitor of NmDapE with a Ki of 2.8 μM. To examine the nature of the interaction of ʟ-captopril with the dinuclear active site of DapE, we have obtained electron paramagnetic resonance (EPR) and magnetic circular dichroism (MCD) data for the enzymatically hyperactive Co(II)-substituted forms of both HiDapE and NmDapE. EPR and MCD data indicate that the two Co(II) ions in DapE are antiferromagnetically coupled, yielding an S = 0 ground state, and suggest a thiolate bridge between the two metal ions. Verification of a thiolate-bridged dinuclear complex was obtained by determining the three-dimensional X-ray crystal structure of NmDapE in complex with ʟ-captopril at 1.8 Å resolution. Combination of these data provides new insights into binding of ʟ-captopril to the active site of DapE enzymes as well as important inhibitor–active site residue interaction’s. Such information is critical for the design of new, potent inhibitors of DapE enzymes

Spitzer Infrared Spectrograph Observations of Magellanic Cloud Planetary Nebulae: the nature of dust in low metallicity circumstellar ejecta

We present 5 - 40 micron spectroscopy of 41 planetary nebulae (PNe) in the Magellanic Clouds, observed with the Infrared Spectrograph on board the Spitzer Space Telescope. The spectra show the presence of a combination of nebular emission lines and solid-state features from dust, superimposed on the thermal IR continuum. By analyzing the 25 LMC and 16 SMC PNe in our sample we found that the IR spectra of 14 LMC and 4 SMC PNe are dominated by nebular emission lines, while the other spectra show solid-state features. We observed that the solid-state features are compatible with carbon-rich dust grains (SiC, polycyclic aromatic hydrocarbons (PAHs), etc.) in most cases, except in three PNe showing oxygen-rich dust features. The frequency of carbonaceous dust features is generally higher in LMC than in SMC PNe. The spectral analysis allowed the correlations of the dust characteristics with the gas composition and morphology, and the properties of the central stars. We found that: 1) all PNe with carbonaceous dust features have C/O>1, none of these being bipolar or otherwise highly asymmetric; 2) all PNe with oxygen-rich dust features have C/O<1, with probable high mass progenitors if derived from single-star evolution (these PNe are either bipolar or highly asymmetric); 3) the dust temperature tracks the nebular and stellar evolution; and 4) the dust production efficiency depends on metallicity, with low metallicity environments not favoring dust production.Comment: The Astrophysical Journal, in pres

Characteristics of aquatic rescues undertaken by bystanders in Australia

An issue of growing importance within the field of drowning prevention is the undertaking of aquatic rescues by bystanders, who sometimes drown in the process. The main objectives of this study were to describe characteristics of bystanders making rescues in different Australian aquatic environments, identify the role of prior water safety training in conducting bystander rescues and provide insights into future public education strategies relating to bystander rescue scenarios. An online survey was disseminated via various social media platforms in 2017 and gathered a total of 243 complete responses. The majority of bystander rescues described took place in coastal waterways (76.5%; n = 186), particularly beaches (n = 67), followed by pools (17.3%; n = 42) and inland waterways (6.2%; n = 15). The majority of respondents were males (64.2%; n = 156) who rescued on average approximately twice as many people in their lifetime (6.5) than female respondents (3.6). Most rescues occurred more than 1 km from lifeguard/lifesaver services (67%; n = 163), but in the presence of others (94.2%; n = 229). The majority of bystander rescuers had water safety training (65.8%; n = 160), self-rated as strong swimmers (68.3%; n = 166), conducted the rescue without help from others (60%; n = 146), did not use a flotation device to assist (63%; n = 153), but were confident in their ability to make the rescue (76.5%; n = 186). However, most considered the situation to be very serious (58%; n = 141) and felt they had saved a life (70.1%; n = 172). With the exception of pools, most bystanders rescued strangers (76.1%; n = 185).While Australia clearly benefits from having a strong water safety culture, there is no clear consensus on the most appropriate actions bystanders should take when confronted with a potential aquatic rescue scenario. In particular, more research is needed to gather information regarding bystander rescues undertaken by those without prior water safety training