Topographic Evolution and Climate Aridification during Continental Collision: Insights from Computer Simulations

How do the feedbacks between tectonics, sediment transport and climate work to shape the topographic evolution of the Earth? This question has been widely addressed via numerical models constrained with thermochronological and geomorphological data at scales ranging from local to orogenic. Here we present a novel numerical model that aims at reproducing the interaction between these processes at the continental scale. For this purpose, we combine in a single computer program: 1) a thin-sheet viscous model of continental deformation; 2) a stream-power surface-transport approach; 3) flexural isostasy allowing for the formation of large sedimentary foreland basins; and 4) an orographic precipitation model that reproduces basic climatic effects such as continentality and rain shadow. We quantify the feedbacks between these processes in a synthetic scenario inspired by the India-Asia collision and the growth of the Tibetan Plateau. We identify a feedback between erosion and crustal thickening leading locally to a <50% increase in deformation rates in places where orographic precipitation is concentrated. This climatically-enhanced deformation takes place preferentially at the upwind flank of the growing plateau, specially at the corners of the indenter (syntaxes). We hypothesize that this may provide clues for better understanding the mechanisms underlying the intriguing tectonic aneurisms documented in the Himalayas. At the continental scale, however, the overall distribution of topographic basins and ranges seems insensitive to climatic factors, despite these do have important, sometimes counterintuitive effects on the amount of sediments trapped within the continent. The dry climatic conditions that naturally develop in the interior of the continent, for example, trigger large intra-continental sediment trapping at basins similar to the Tarim Basin because they determine its endorheic/exorheic drainage. These complex climatic-drainage-tectonic interactions make the development of steady-state topography at the continental scale unlikely.     

Brownian Dynamics Computer Simulations of Quenched Lennard-Jones-like Fluids: I Morphology and Local Structural Evolution

Abstract

The structural characteristics during phase separation of a model colloidal system were investigated using Brownian dynamics simulation. The structures that formed were analysed using the radial distribution function and structure factor in separate time periods after the quench. The data were interpreted in terms of scale-invariancy and density inhomogeneities. The systems, which consisted of a gas-like phase and dense liquid or solid-like regions, developed with a highly interconnected morphology during the simulations. The aggregate morphology was sensitive to the range of the attractive part of the potential and the position in the phase diagram after the quench. The long-range 12:6 potential induced compact structures with thick filaments, whereas the systems generated using the shorter-ranged 24:12 and 36:18 potentials persisted in a more diffuse network and also evolved more slowly with time. The fractal dimensions were quite high, typically close to 3. The 24:12 and 36:18 potential systems developed regions of local crystalline order which formed contemporaneously with the more global morphological changes. In contrast, at low temperatures the particles of the longer-range 12:6 potential became trapped in glass-like states during the course of the morphological changes in the system. The value of the characteristic lengthscale with time exponent, α, was found to be dependent on the temperature, density and interaction potential and therefore cannot be described as ‘universal’.     

Evolution of Stronger SARS-CoV-2 Variants as Revealed Through the Lens of Molecular Dynamics Simulations

The Protein Journal - Using molecular dynamics simulations, the protein–protein interactions of the receptor-binding domain of the wild-type and seven variants of the severe acute respiratory...     

The Double Bind: Performing Arts in Hongkong

In Hongkong, local identity is muted not only by the master narrative of ‘history of Europe’, but by that of ‘Chinese history’ and ‘Chinese civilization’. This comprises a ‘double bind’ on those who write and present drama, and the dance. This paper examines the way in which the two master narratives both conflict and assist one another in the elite performing arts. It points a schematic model which tries to take account of the self-conscious efforts of some local intelligentsia to insert a specifically Hongkong dimension between the two master narratives. This cultural refiguration has much to do with the sense of instability and concern for the future which has recently gripped the island.     

Performing arts medicine.

Arts medicine has come of age, resulting from 3 important developments over the past decade: improved methods of diagnosis and treatment, an awareness that artists suffer from special problems related to their occupation and lifestyle, and the establishment of health programs emphasizing an interdisciplinary approach to these patients. We focus on the patterns of illness afflicting performing artists, specifically dancers, singers, actors, and instrumental musicians, and explain some of the things a health care team can do in treating these patients. The conditions governing these patients'' lives--early exposure to high expectations of excellence, incessant demands for perfection, long periods of intense practicing, fierce competition, high levels of anxiety associated with performance, and uncertain careers--need to be understood. Levels of disease and disability are remarkably high, but artists often ignore symptoms. We discuss the musculoskeletal, neurologic, vocal, psychological, and other syndromes found among performers and some of the difficulties in treating them. The prevention of injury, conservative management, collaboration with teachers, and a psychotherapeutic approach are desirable. Arts medicine programs for professional consultation exist in several major cities of the United States and abroad. Although research is needed regarding the effectiveness of health care services for performing artists, the scientific literature devoted to this field is growing.     

Mechanosensitive Channels: Insights from Continuum-Based Simulations

Mechanotransduction plays an important role in regulating cell functions and it is an active topic of research in biophysics. Despite recent advances in experimental and numerical techniques, the intrinsic multiscale nature imposes tremendous challenges for revealing the working mechanisms of mechanosensitive channels. Recently, a continuum-mechanics-based hierarchical modeling and simulation framework has been established and applied to study the mechanical responses and gating behaviors of a prototypical mechanosensitive channel, the mechanosensitive channel of large conductance (MscL) in bacteria Escherichia coli (E. coli), from which several putative gating mechanisms have been tested and new insights are deduced. This article reviews these latest findings using the continuum mechanics framework and suggests possible improvements for future simulation studies. This computationally efficient and versatile continuum-mechanics-based protocol is poised to make contributions to the study of a variety of mechanobiology problems.     

Simulations of a protein translocation pore: SecY

SecY is the central channel protein of the SecYEbeta translocon, the structure of which has been determined by X-ray diffraction. Extended (15 ns) MD simulations of the isolated SecY protein in a phospholipid bilayer have been performed to explore the relationship between protein flexibility and the mechanisms of channel gating. In particular, principal components analysis of the simulation trajectory has been used to probe the intrinsic flexibility of the isolated SecY protein in the absence of the gamma-subunit (SecE) clamp. Analysis and visualization of the principal eigenvectors support a "plug and clamshell" model of SecY channel gating. The simulation results also indicate that hydrophobic gating at the central pore ring prevents leakage of water and ions through the channel in the absence of a translocating peptide.     

Effects of Continuous Low Dose-Rate Irradiation: Computer Simulations

Abstract. The effects of continuous low dose-rate irradiation are studied with a computer model that incorporates cell kinetics and the accumulation and repair of radiation damage. This theoretical approach independently explores the effects on survival curves of a phase block, inherited damage and proliferation by dying cells. the computer model is a Monte Carlo simulation which follows the evolution in time of the family trees of a growing cell population under continuous irradiation. the model uses as input the measured phase-specific survival curves for acute exposures and the cell kinetic parameters to generate survival curves for continous low dose-rate irradiations. Cell survival curves for Chinese hamster lung cells (V79) for dose rates ranging from 15 to 500 cGy/h have been generated using various model assumptions. the model shows that for these cells a G₂ block will maximize cell killing for an optimum dose rate near 75 cGy/h. the effect on survival curves of inherited damage, as well as that of the proliferation by dying cells, is shown to increase monotonically with decreasing dose rates, and to be quite large at low dose rates.     

Lipid Simulations: A Perspective on Lipids in Action

In this article, we provide an overview of lipid simulations, describing how a computer can be used as a laboratory for lipid research. We briefly discuss the methodology of lipid simulations followed by a number of topical applications that show the benefit of computer modeling for complementing experiments. In particular, we show examples of cases in which simulations have made predictions of novel phenomena that have later been confirmed by experimental studies. Overall, the applications discussed in this article focus on the most recent state of the art and aim to provide a perspective of where the field of lipid simulations stands at the moment.Lipids are very diverse in their structures and functions (Sackmann 1995; Mouritsen 2005; van Meer 2005). They are a crucial component of numerous biological entities such as membranes, lipoprotein particles, and lipid droplets, and they are involved in numerous cellular functions related to, for example, signaling and energy storage. Importantly, as lipids also compartmentalize biological membranes by creating membrane domains with different physical properties, lipids also affect or even govern membrane proteins and their functionality (McIntosh and Simon 2006; Lingwood and Simons 2010).Although experiments are the cornerstone of lipid research, they are limited in resolution, permitting one to unravel biological phenomena only to a limited extent. Especially difficult to deal with are molecular scales with an objective to probe phenomena in the nanometer regime over timescales less than a microsecond. Molecular simulations, on the other hand, have no such limits with regard to resolution. Validated simulation models can be used to consider all sorts of phenomena, ranging from selectivity of ion channels to interactions of lipids with membrane proteins, and further to nonequilibrium lipid trafficking and domain as well as pore formation (Bjelkmar 2009; Bucher et al. 2010; Fan et al. 2010a,b).The first simulations of lipid systems were performed in the early 1980s (Kox et al. 1980; van der Ploeg and Berendsen 1982, 1983). Starting from those times when solvent-free membranes composed of 32 lipids were simulated for about 80 picoseconds (van der Ploeg and Berendsen 1982), the field of lipid simulations has matured to a stage in which the scales simulated in atomistic detail cover tens of nanometers (about 10⁵–10⁶ atoms) and several microseconds (Bjelkmar 2009; Dror 2009). This progress in atomistic simulations has been supported by the development of coarse-grained models and multiscale simulation techniques able to elucidate phenomena over scales much larger than the molecular ones (Ayton and Voth 2009; Murtola et al. 2009). The currently used particle-based coarse-grained models are appropriate for studies of systems of millions of particles over timescales of the order of 10–100 microseconds (Reynwar et al. 2007; Apajalahti 2010), and the situation continuously improves. Today, simulations can provide a great deal of insight into a variety of phenomena that are not tractable by experiments. Simulations are no longer used as tools for confirming what has been found in experiments; instead they have predictive power, guiding experiments to focus on novel phenomena. Current aims to bridge molecular simulations with computational systems biology foster the field further, coupling molecular and cellular phenomena to one another.In this article, we provide an overview of lipid simulations, describing how a computer can be used as a laboratory for lipid research. We briefly discuss the methodology of lipid simulations followed by a number of topical applications that show the benefit of simulations. The applications given here as examples of simulations’ role for lipid research focus on the most recent state of the art and aim to provide a perspective of where we stand at the moment. A brief discussion of the prospects of lipid simulations closes this article.     

First-Principles Protein Folding Simulations

Abstract

It is widely believed that the prediction of the three-dimensional structures of proteins from the first principles is impossible. This view is based on the fact that the number of possible structures for each protein is astronomically large. The question is then why a protein folds into its native structure with the proper biological functions in the time scale of milliseconds to minutes, and this is called Levinthal's paradox. In this article I will discuss our strategy for attacking the protein folding problem. Our approach consists of two elements: the inclusion of accurate solvent effects and the development of powerful simulation algorithms that can avoid getting trapped in states of energy local minima. For the former, we discuss several models varying in nature from crude (distance-dependent dielectric function) to rigorous (reference interaction site model). For the latter, we show the effectiveness of Monte Carlo simulated annealing and generalized-ensemble algorithms.