Gas Enrichment at Liquid-Wall Interfaces

Molecular dynamics simulations of Lennard-Jones systems are performed to study the effects of dissolved gas on liquid-wall and liquid-gas interfaces. Gas enrichment at walls is observed which for hydrophobic walls can exceed more than two orders of magnitude when compared to the gas density in the bulk liquid. As a consequence, the liquid structure close to the wall is considerably modified, leading to an enhanced wall slip. At liquid-gas interfaces gas enrichment is found which reduces the surface tension.Comment: main changes compared to version 1: flow simulations are included as well as different types of gase

Sites of Cultural Production in Response to Mass Extinction

This conversation, mediated by Tara Nicholson, considers Stephanie Turner and EvaMarie Lindahl’s research in cultural representations of extinction and investigations of more-than-human forms of storytelling through an art historical lens. In response to Lori Gruen’s classification, extinction is a distinctive loss of ‘animal cultures’. It is more than biodiversity destruction or a static inventory of a species’ death. Nonhuman ways of building bonds, reproducing, teaching offspring, constructing homes and mourning the dead, are all systems of knowledge lost in extinction (Gruen et al. 2017). This conversation offers compassionate ways of bearing witness to species destruction and a space for empathy and kinship. The authors ask, how can dialogue between science and art lead to new understandings of the ‘wicked problem’ of mass extinction during climate crisis? Examining methodologies of cross-disciplinary storytelling and cultural production, this exchange connects museum practice, large-scale public artworks and artistic research as types of embodied knowledge to promote public awareness surrounding the acceleration of species extinction

310-Helix Conformation Facilitates the Transition of a Voltage Sensor S4 Segment toward the Down State

AbstractThe activation of voltage-gated ion channels is controlled by the S4 helix, with arginines every third residue. The x-ray structures are believed to reflect an open-inactivated state, and models propose combinations of translation, rotation, and tilt to reach the resting state. Recently, experiments and simulations have independently observed occurrence of 310-helix in S4. This suggests S4 might make a transition from α- to 310-helix in the gating process. Here, we show 310-helix structure between Q1 and R3 in the S4 segment of a voltage sensor appears to facilitate the early stage of the motion toward a down state. We use multiple microsecond-steered molecular simulations to calculate the work required for translating S4 both as α-helix and transformed to 310-helix. The barrier appears to be caused by salt-bridge reformation simultaneous to R4 passing the F233 hydrophobic lock, and it is almost a factor-two lower with 310-helix. The latter facilitates translation because R2/R3 line up to face E183/E226, which reduces the requirement to rotate S4. This is also reflected in a lower root mean-square deviation distortion of the rest of the voltage sensor. This supports the 310 hypothesis, and could explain some of the differences between the open-inactivated- versus activated-states

Glass transition in biomolecules and the liquid-liquid critical point of water

Using molecular dynamics simulations, we investigate the relation between the dynamic transitions of biomolecules (lysozyme and DNA) and the dynamic and thermodynamic properties of hydration water. We find that the dynamic transition of the macromolecules, sometimes called a ``protein glass transition'', occurs at the temperature of dynamic crossover in the diffusivity of hydration water, and also coincides with the maxima of the isobaric specific heat $C_P$ and the temperature derivative of the orientational order parameter. We relate these findings to the hypothesis of a liquid-liquid critical point in water. Our simulations are consistent with the possibility that the protein glass transition results from crossing the Widom line, which is defined as the locus of correlation length maxima emanating from the hypothesized second critical point of water.Comment: 10 Pages, 12 figure

Mixed quantum-classical dynamics of an amide-I vibrational excitation in a protein a-helix

Adenosine triphosphate sATPd is known to be the main energy currency of the living cell, and is used as a coenzyme to generate energy for many cellular processes through hydrolysis to adenosine diphosphate sADPd,although the mechanism of energy transfer is not well understood. It has been proposed that following hydrolysis of the ATP cofactor bound to a protein, up to two quanta of amide-I vibrational energy are excited and utilized to bring about important structural changes in the protein. To study whether, and how, amide-I vibrational excitations are capable of leading to protein structural changes, we have added components arising from quantum-mechanical amide-I vibrational excitations to the total energy and force terms within a moleculardynamics simulation. This model is applied to helical deca-alanine as a test case to investigate how its dynamics differs in the presence or absence of an amide-I excitation. We find that the presence of an amide-I excitation can bias the structure toward a more helical state

Genetic steps to organ laterality in zebrafish.

All internal organs are asymmetric along the left-right axis. Here we report a genetic screen to discover mutations which perturb organ laterality. Our particular focus is upon whether, and how, organs are linked to each other as they achieve their laterally asymmetric positions. We generated mutations by ENU mutagenesis and examined F3 progeny using a cocktail of probes that reveal early primordia of heart, gut, liver and pancreas. From the 750 genomes examined, we isolated seven recessive mutations which affect the earliest left-right positioning of one or all of the organs. None of these mutations caused discernable defects elsewhere in the embryo at the stages examined. This is in contrast to those mutations we reported previously (Chen et al., 1997) which, along with left-right abnormalities, cause marked perturbation in gastrulation, body form or midline structures. We find that the mutations can be classified on the basis of whether they perturb relationships among organ laterality. In Class 1 mutations, none of the organs manifest any left-right asymmetry. The heart does not jog to the left and normally leftpredominant BMP4 in the early heart tube remains symmetric. The gut tends to remain midline. There frequently is a remarkable bilateral duplication of liver and pancreas. Embryos with Class 2 mutations have organotypic asymmetry but, in any given embryo, organ positions can be normal, reversed or randomized. Class 3 reveals a hitherto unsuspected gene that selectively affects laterality of heart. We find that visceral organ positions are predicted by the direction of the preceding cardiac jog. We interpret this as suggesting that normally there is linkage between cardiac and visceral organ laterality. Class 1 mutations, we suggest, effectively remove the global laterality signals, with the consequence that organ positions are effectively symmetrical. Embryos with Class 2 mutations do manifest linkage among organs, but it may be reversed, suggesting that the global signals may be present but incorrectly orientated in some of the embryos. That laterality decisions of organs may be independently perturbed, as in the Class 3 mutation, indicates that there are distinctive pathways for reception and organotypic interpretation of the global signals

Strong pressure-energy correlations in van der Waals liquids

Strong correlations between equilibrium fluctuations of the configurational parts of pressure and energy are found in the Lennard-Jones liquid and other simple liquids, but not in hydrogen-bonding liquids like methanol and water. The correlations, that are present also in the crystal and glass phases, reflect an effective inverse power-law repulsive potential dominating fluctuations, even at zero and slightly negative pressure. In experimental data for supercritical Argon, the correlations are found to be approximately 96%. Consequences for viscous liquid dynamics are discussed.Comment: Phys. Rev. Lett., in pres

TDP1 deficiency sensitizes human cells to base damage via distinct topoisomerase I and PARP mechanisms with potential applications for cancer therapy

Base damage and topoisomerase I (Top1)-linked DNA breaks are abundant forms of endogenous DNA breakage, contributing to hereditary ataxia and underlying the cytotoxicity of a wide range of anti-cancer agents. Despite their frequency, the overlapping mechanisms that repair these forms of DNA breakage are largely unknown. Here, we report that depletion of Tyrosyl DNA phosphodiesterase 1 (TDP1) sensitizes human cells to alkylation damage and the additional depletion of apurinic/apyrimidinic endonuclease I (APE1) confers hypersensitivity above that observed for TDP1 or APE1 depletion alone. Quantification of DNA breaks and clonogenic survival assays confirm a role for TDP1 in response to base damage, independently of APE1. The hypersensitivity to alkylation damage is partly restored by depletion of Top1, illustrating that alkylating agents can trigger cytotoxic Top1-breaks. Although inhibition of PARP activity does not sensitize TDP1-deficient cells to Top1 poisons, it confers increased sensitivity to alkylation damage, highlighting partially overlapping roles for PARP and TDP1 in response to genotoxic challenge. Finally, we demonstrate that cancer cells in which TDP1 is inherently deficient are hypersensitive to alkylation damage and that TDP1 depletion sensitizes glioblastoma-resistant cancer cells to the alkylating agent temozolomide