Towards Automated Benchmarking of Atomistic Forcefields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive

Atomistic molecular simulations are a powerful way to make quantitative predictions, but the accuracy of these predictions depends entirely on the quality of the forcefield employed. While experimental measurements of fundamental physical properties offer a straightforward approach for evaluating forcefield quality, the bulk of this information has been tied up in formats that are not machine-readable. Compiling benchmark datasets of physical properties from non-machine-readable sources require substantial human effort and is prone to accumulation of human errors, hindering the development of reproducible benchmarks of forcefield accuracy. Here, we examine the feasibility of benchmarking atomistic forcefields against the NIST ThermoML data archive of physicochemical measurements, which aggregates thousands of experimental measurements in a portable, machine-readable, self-annotating format. As a proof of concept, we present a detailed benchmark of the generalized Amber small molecule forcefield (GAFF) using the AM1-BCC charge model against measurements (specifically bulk liquid densities and static dielectric constants at ambient pressure) automatically extracted from the archive, and discuss the extent of available data. The results of this benchmark highlight a general problem with fixed-charge forcefields in the representation low dielectric environments such as those seen in binding cavities or biological membranes

Virtue and austerity

Virtue ethics is often proposed as a third way in health-care ethics, that while consequentialism and deontology focus on action guidelines, virtue focuses on character; all three aim to help agents discern morally right action although virtue seems to have least to contribute to political issues, such as austerity. I claim: (1) This is a bad way to characterize virtue ethics. The 20th century renaissance of virtue ethics was first proposed as a response to the difficulty of making sense of ‘moral rightness’ outside a religious context. For Aristotle the right action is that which is practically best; that means best for the agent in order to live a flourishing life.There are no moral considerations besides this. (2) Properly characterized, virtue ethics can contribute to discussion of austerity. A criticism of virtue ethics is that fixed characteristics seem a bad idea in ever-changing environments; perhaps we should be generous in prosperity, selfish in austerity. Furthermore, empirical evidence suggests that people indeed do change with their environment. However, I argue that virtues concern fixed values not fixed behaviour; the values underlying virtue allow for different behaviour in different circumstances: in austerity, virtues still give the agent the best chance of flourishing. Two questions arise. (a) In austere environments might not injustice help an individual flourish by, say, obtaining material goods? No, because unjust acts undermine the type of society the agent needs for flourishing. (b) What good is virtue to those lacking the other means to flourish? The notion of degrees of flourishing shows that most people would benefit somewhat from virtue. However, in extreme circumstances virtue might harm rather than benefit the agent: such circumstances are to be avoided; virtue ethics thus has a political agenda to enable flourishing. This requires justice, a fortiori when in austerity

Coherent Error Suppression in Multi-Qubit Entangling Gates

We demonstrate a simple pulse shaping technique designed to improve the fidelity of spin-dependent force operations commonly used to implement entangling gates in trapped-ion systems. This extension of the M{\o}lmer-S{\o}rensen gate can theoretically suppress the effects of certain frequency and timing errors to any desired order and is demonstrated through Walsh modulation of a two-qubit entangling gate on trapped atomic ions. The technique is applicable to any system of qubits coupled through collective harmonic oscillator modes

A double dissociation between anterior and posterior superior temporal gyrus for processing audiovisual speech demonstrated by electrocorticography

Human speech can be comprehended using only auditory information from the talker's voice. However, comprehension is improved if the talker's face is visible, especially if the auditory information is degraded as occurs in noisy environments or with hearing loss. We explored the neural substrates of audiovisual speech perception using electrocorticography, direct recording of neural activity using electrodes implanted on the cortical surface. We observed a double dissociation in the responses to audiovisual speech with clear and noisy auditory component within the superior temporal gyrus (STG), a region long known to be important for speech perception. Anterior STG showed greater neural activity to audiovisual speech with clear auditory component, whereas posterior STG showed similar or greater neural activity to audiovisual speech in which the speech was replaced with speech-like noise. A distinct border between the two response patterns was observed, demarcated by a landmark corresponding to the posterior margin of Heschl's gyrus. To further investigate the computational roles of both regions, we considered Bayesian models of multisensory integration, which predict that combining the independent sources of information available from different modalities should reduce variability in the neural responses. We tested this prediction by measuring the variability of the neural responses to single audiovisual words. Posterior STG showed smaller variability than anterior STG during presentation of audiovisual speech with noisy auditory component. Taken together, these results suggest that posterior STG but not anterior STG is important for multisensory integration of noisy auditory and visual speech

Variability of Pennsylvanian-Permian Carbonate Associations and Implications for NW Pangea Palaeogeography, East-Central British Columbia, Canada

Different stages of Pennsylvanian-Permian carbonate sedimentation in east-central British Columbia record a complex history of changing environments influenced by evolving palaeogeography and climate. Newly recognized tectonically controlled features affected the distribution and variability of carbonate associations, providing new interpretations for this portion of the west coast of Pangea. Both a heterozoan (cool water) and photozoan (warm-water) association were identified on either side of a palaeogeographic high here informally termed “Tipinahokan Peninsula”. Cool water carbonates were located outboard, or to the west of this high, an area influenced by upwelling waters. Inboard of this high, a warm, protected sea developed, here termed “Kisosowin Sea”. This configuration and palaeolatitude is similar to that of Baja California, Mexico and the Sea of Cortéz, providing a good modern analog for these deposits where warm water carbonates grow at latitudes otherwise dominated by cool water deposits. The warm sea provided a place for a photozoan association to develop during the Permian when the low latitude NW coast of Pangea was dominated by cool water carbonates

Interfacial Reactions of Ozone with Surfactant Protein B in a Model Lung Surfactant System

Oxidative stresses from irritants such as hydrogen peroxide and ozone (O_3) can cause dysfunction of the pulmonary surfactant (PS) layer in the human lung, resulting in chronic diseases of the respiratory tract. For identification of structural changes of pulmonary surfactant protein B (SP-B) due to the heterogeneous reaction with O_3, field-induced droplet ionization (FIDI) mass spectrometry has been utilized. FIDI is a soft ionization method in which ions are extracted from the surface of microliter-volume droplets. We report structurally specific oxidative changes of SP-B_(1−25) (a shortened version of human SP-B) at the air−liquid interface. We also present studies of the interfacial oxidation of SP-B_(1−25) in a nonionizable 1-palmitoyl-2-oleoyl-sn-glycerol (POG) surfactant layer as a model PS system, where competitive oxidation of the two components is observed. Our results indicate that the heterogeneous reaction of SP-B_(1−25) at the interface is quite different from that in the solution phase. In comparison with the nearly complete homogeneous oxidation of SP-B_(1−25), only a subset of the amino acids known to react with ozone are oxidized by direct ozonolysis in the hydrophobic interfacial environment, both with and without the lipid surfactant layer. Combining these experimental observations with the results of molecular dynamics simulations provides an improved understanding of the interfacial structure and chemistry of a model lung surfactant system subjected to oxidative stress

A microfluidic-based bubble generation platform enables analysis of physical property change in phospholipid surfactant layers by interfacial ozone reaction

The air-liquid interface filled with pulmonary surfactant is a unique feature of our lung alveoli. The mechanical properties of this interface play an important role in breathing and its malfunction induced by an environmental hazard, such as ozone, relates to various lung diseases. In order to understand the interfacial physics of the pulmonary surfactant system, we employed a microfluidic bubble generation platform with a model pulmonary surfactant composed of two major phospholipids: DPPC (1,2-dipalmitoyl-sn-phosphatidylcholine) and POPG (1-palmitoyl-2-oleoyl-sn-phosphatidylglycerol). With fluorescence imaging, we observed the ozone-induced chemical modification of the unsaturated lipid component of the lipid mixture, POPG. This chemical change due to the oxidative stress was further utilized to study the physical characteristics of the interface through the bubble formation process. The physical property change was evaluated through the oscillatory behaviour of the monolayer, as well as the bubble size and formation time. The results presented demonstrate the potential of this platform to study interfacial physics of lung surfactant system under various environmental challenges, both qualitatively and quantitatively

The problem of mutually unbiased bases in dimension 6

We outline a discretization approach to determine the maximal number of mutually unbiased bases in dimension 6. We describe the basic ideas and introduce the most important definitions to tackle this famous open problem which has been open for the last 10 years. Some preliminary results are also listed

Reverse evolution of armor plates in the threespine stickleback.

Faced with sudden environmental changes, animals must either adapt to novel environments or go extinct. Thus, study of the mechanisms underlying rapid adaptation is crucial not only for the understanding of natural evolutionary processes but also for the understanding of human-induced evolutionary change, which is an increasingly important problem [1-8]. In the present study, we demonstrate that the frequency of completely plated threespine stickleback fish (Gasterosteus aculeatus) has increased in an urban freshwater lake (Lake Washington, Seattle, Washington) within the last 40 years. This is a dramatic example of "reverse evolution,"[9] because the general evolutionary trajectory is toward armor-plate reduction in freshwater sticklebacks [10]. On the basis of our genetic studies and simulations, we propose that the most likely cause of reverse evolution is increased selection for the completely plated morph, which we suggest could result from higher levels of trout predation after a sudden increase in water transparency during the early 1970s. Rapid evolution was facilitated by the existence of standing allelic variation in Ectodysplasin (Eda), the gene that underlies the major plate-morph locus [11]. The Lake Washington stickleback thus provides a novel example of reverse evolution, which is probably caused by a change in allele frequency at the major plate locus in response to a changing predation regime

The role of brand loyalty and social media in e-commerce interfaces: survey results and implications for user interfaces

This paper explores the role of brand loyalty and social media in e-commerce interfaces. A survey consisting of 118 respondents was contacted to address the questions relating to online shopping and brand loyalty. Link between the frequency of access and time spent on an e-commerce user interface, and brand loyalty, gender and age profile differences, and the role of social media to branding and on-line shopping was analyzed. It was found that online loyalty differs from offline loyalty and loyalty also differed across genders, showing men were more loyal than women when shopping online. Information shared about products on social media by friends and family played an important role in purchase decision making. Website interface and ease of navigation were also key aspects for online shopping. The research concluded with recommendations to create multimodal websites which are more interactive and targeted so customer experience is enhanced and loyalty is achieved through the use of interactivity and social media