Effect of Cluster Formation on Isospin Asymmetry in the Liquid-Gas Phase Transition Region

Nuclear matter within the liquid-gas phase transition region is investigated in a mean-field two-component Fermi-gas model. Following largely analytic considerations, it is shown that: (1) Due to density dependence of asymmetry energy, some of the neutron excess from the high-density phase could be expelled into the low-density region. (2) Formation of clusters in the gas phase tends to counteract this trend, making the gas phase more liquid-like and reducing the asymmetry in the gas phase. Flow of asymmetry between the spectator and midrapidity region in reactions is discussed and a possible inversion of the flow direction is indicated.Comment: 9 pages,3 figures, RevTe

Adaptive Accelerated Molecular Dynamics (Ad-AMD) Revealing the Molecular Plasticity of P450cam

An extended accelerated molecular dynamics (AMD) methodology called adaptive AMD is presented. Adaptive AMD (Ad-AMD) is an efficient and robust conformational space sampling algorithm that is particularly-well suited to proteins with highly structured potential energy surfaces exhibiting complex, large-scale collective conformational transitions. Ad-AMD simulations of substrate-free P450cam reveal that this system exists in equilibrium between a fully and partially open conformational state. The mechanism for substrate binding depends on the size of the ligand. Larger ligands enter the P450cam binding pocket, and the resulting substrate-bound system is trapped in an open conformation via a population shift mechanism. Small ligands, which fully enter the binding pocket, cause an induced-fit mechanism, resulting in the formation of an energetically stable closed conformational state. These results are corroborated by recent experimental studies and potentially provide detailed insight into the functional dynamics and conformational behavior of the entire cytochrome-P450 superfamily

Latitudinal diversity gradients in Mesozoic non-marine turtles

© 2016 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited. The attached file is the published version of the article

Disease-Associated Mutations Disrupt Functionally Important Regions of Intrinsic Protein Disorder

The effects of disease mutations on protein structure and function have been extensively investigated, and many predictors of the functional impact of single amino acid substitutions are publicly available. The majority of these predictors are based on protein structure and evolutionary conservation, following the assumption that disease mutations predominantly affect folded and conserved protein regions. However, the prevalence of the intrinsically disordered proteins (IDPs) and regions (IDRs) in the human proteome together with their lack of fixed structure and low sequence conservation raise a question about the impact of disease mutations in IDRs. Here, we investigate annotated missense disease mutations and show that 21.7% of them are located within such intrinsically disordered regions. We further demonstrate that 20% of disease mutations in IDRs cause local disorder-to-order transitions, which represents a 1.7–2.7 fold increase compared to annotated polymorphisms and neutral evolutionary substitutions, respectively. Secondary structure predictions show elevated rates of transition from helices and strands into loops and vice versa in the disease mutations dataset. Disease disorder-to-order mutations also influence predicted molecular recognition features (MoRFs) more often than the control mutations. The repertoire of disorder-to-order transition mutations is limited, with five most frequent mutations (R→W, R→C, E→K, R→H, R→Q) collectively accounting for 44% of all deleterious disorder-to-order transitions. As a proof of concept, we performed accelerated molecular dynamics simulations on a deleterious disorder-to-order transition mutation of tumor protein p63 and, in agreement with our predictions, observed an increased α-helical propensity of the region harboring the mutation. Our findings highlight the importance of mutations in IDRs and refine the traditional structure-centric view of disease mutations. The results of this study offer a new perspective on the role of mutations in disease, with implications for improving predictors of the functional impact of missense mutations

A Suite of Early Eocene (~55 Ma) Climate Model Boundary Conditions

We describe a set of early Eocene (~ 55 Ma) climate model boundary conditions constructed in a self-consistent reference frame and incorporating recent data and methodologies. Given the growing need for uniform experimental design within the Eocene climate modelling community and the challenges faced in simulating the prominent features of Eocene climate, we make publicly available our data sets of Eocene topography, bathymetry, tidal dissipation, vegetation, aerosol distributions and river runoff. Major improvements in our boundary conditions over previous efforts include the implementation of the ANTscape palaeotopography of Antarctica, more accurate representations of the Drake Passage and Tasman Gateway, as well as an approximation of sub grid cell topographic variability. Our boundary conditions also include for the first time modelled estimates of Eocene aerosol distributions and tidal dissipation, both consistent with our palaeotopography and palaeobathymetry. The resolution of our data sets is unprecedented and will facilitate high resolution climate simulations. In light of the inherent uncertainties involved in reconstructing global boundary conditions for past time periods these data sets should be considered as one interpretation of the available data and users are encouraged to modify them according to their needs and interpretations. This paper marks the beginning of a process for reconstructing a set of accurate, open-access Eocene boundary conditions for use in climate models

Morphology of Shocked Lateral Outflows in Colliding Hydrodynamic Flows

Supersonic interacting flows occurring in phenomena such as protostellar jets give rise to strong shocks, and have been demonstrated in several laboratory experiments. To study such colliding flows, we use the AstroBEAR AMR code to conduct hydrodynamic simulations in three dimensions. We introduce variations in the flow parameters of density, velocity, and cross sectional radius of the colliding flows %radius in order to study the propagation and conical shape of the bow shock formed by collisions between two, not necessarily symmetric, hypersonic flows. We find that the motion of the interaction region is driven by imbalances in ram pressure between the two flows, while the conical structure of the bow shock is a result of shocked lateral outflows (SLOs) being deflected from the horizontal when the flows are of differing cross-section

Cooling and Instabilities in Colliding Radiative Flows with Toroidal Magnetic Fields

We report on the results of a simulation based study of colliding magnetized plasma flows. Our set-up mimics pulsed power laboratory astrophysical experiments but, with an appropriate frame change, are relevant to astrophysical jets with internal velocity variations. We track the evolution of the interaction region where the two flows collide. Cooling via radiative loses are included in the calculation. We systematically vary plasma beta ($\beta_m$) in the flows, the strength of the cooling ($\Lambda_0$) and the exponent ($\alpha$) of temperature-dependence of the cooling function. We find that for strong magnetic fields a counter-propagating jet called a "spine" is driven by pressure from shocked toroidal fields. The spines eventually become unstable and break apart. We demonstrate how formation and evolution of the spines depends on initial flow parameters and provide a simple analytic model that captures the basic features of the flow.Comment: 14 pages, 16 figures. Submitted to MNRA