Rigidity analysis of HIV-1 protease

We present a rigidity analysis on a large number of X-ray crystal structures of the enzyme HIV-1 protease using the 'pebble game' algorithm of the software FIRST. We find that although the rigidity profile remains similar across a comprehensive set of high resolution structures, the profile changes significantly in the presence of an inhibitor. Our study shows that the action of the inhibitors is to restrict the flexibility of the beta-hairpin flaps which allow access to the active site. The results are discussed in the context of full molecular dynamics simulations as well as data from NMR experiments.Comment: 4 pages, 3 figures. Conference proceedings for CMMP conference 2010 which was held at the University of Warwic

Clay Sediments from Basaltic Terrains: Implications for Sedimentary Processes on Mars

The Mars Science Laboratory (MSL) rover, Curiosity, has been traversing across fluvial, lacustrine, and eolian sedimentary rocks since it touched down in 2012. The CheMin X-ray diffractometer (XRD) on board Curiosity has revealed smectite clay minerals in most fluvio-lacustrine samples and abundant X-ray amorphous materials in all samples analyzed to date. For example, mudstones from the Sheepbed member at the base of the stratigraphic section and the lower part of the Murray formation contain on average ~7 to 20 wt% smectite and ~30 to 46 wt% X-ray amorphous abundances. On Earth, smectite and secondary X-ray amorphous materials are juvenile weathering products that are generated in sedimentary environments and ultimately record the interaction between primary igneous minerals and the hydrosphere, atmosphere, and biosphere. For this study, we investigated glacio-fluvio-eolian sediments generated in basaltic terrains as terrestrial analogs for the mudstones from Gale Crater, Mars. This work focuses on the clay sized sediments (<2 m) from these deposits as this grain size hosts the most mineralogically and geochemically altered detritus in sedimentary environments. The goal of investigating basaltic sedimentation is to create a terrestrial reference frame that sheds light on the paleoclimate and paleoaqueous conditions responsible for shaping the ancient sedimentary environments of Mars (e.g., Gale Crater and Jezero Crater)

Gas permeation through a polymer network

We study the diffusion of gas molecules through a two-dimensional network of polymers with the help of Monte Carlo simulations. The polymers are modeled as non-interacting random walks on the bonds of a two-dimensional square lattice, while the gas particles occupy the lattice cells. When a particle attempts to jump to a nearest-neighbor empty cell, it has to overcome an energy barrier which is determined by the number of polymer segments on the bond separating the two cells. We investigate the gas current $J$ as a function of the mean segment density $\rho$, the polymer length $\ell$ and the probability $q^{m}$ for hopping across $m$ segments. Whereas $J$ decreases monotonically with $\rho$ for fixed $\ell$, its behavior for fixed $\rho$ and increasing $\ell$ depends strongly on $q$. For small, non-zero $q$, $J$ appears to increase slowly with $\ell$. In contrast, for $q=0$, it is dominated by the underlying percolation problem and can be non-monotonic. We provide heuristic arguments to put these interesting phenomena into context.Comment: Dedicated to Lothar Schaefer on the occasion of his 60th birthday. 11 pages, 3 figure

Hopping on the Bethe lattice: Exact results for densities of states and dynamical mean-field theory

We derive an operator identity which relates tight-binding Hamiltonians with arbitrary hopping on the Bethe lattice to the Hamiltonian with nearest-neighbor hopping. This provides an exact expression for the density of states (DOS) of a non-interacting quantum-mechanical particle for any hopping. We present analytic results for the DOS corresponding to hopping between nearest and next-nearest neighbors, and also for exponentially decreasing hopping amplitudes. Conversely it is possible to construct a hopping Hamiltonian on the Bethe lattice for any given DOS. These methods are based only on the so-called distance regularity of the infinite Bethe lattice, and not on the absence of loops. Results are also obtained for the triangular Husimi cactus, a recursive lattice with loops. Furthermore we derive the exact self-consistency equations arising in the context of dynamical mean-field theory, which serve as a starting point for studies of Hubbard-type models with frustration.Comment: 14 pages, 9 figures; introduction expanded, references added; published versio

Decorrelation Stretches (DCS) of Visible Images as a Tool for Sedimentary Provenance Investigations on Earth and Mars

The surface of Mars exhibits vast expanses of mafic sediments and ancient sedimentary rocks that record signals of climate and environment. To decipher the paleoenvironments, the sediment sources and transport histories must be con-strained, but it is not well known how physical fractionation and aqueous alteration affect mafic sediments during glacial, eolian, and fluvial processes. Semi-Autonomous Navigation for Detrital Environments (SAND-E), a NASA Planetary Science and Technology through Analog Research (PSTAR) project, bridges this gap through studies of sediment-grain properties and mineralogy in the glacio-XRD)-derived mineralogies

Floppy modes and the free energy: Rigidity and connectivity percolation on Bethe Lattices

We show that negative of the number of floppy modes behaves as a free energy for both connectivity and rigidity percolation, and we illustrate this result using Bethe lattices. The rigidity transition on Bethe lattices is found to be first order at a bond concentration close to that predicted by Maxwell constraint counting. We calculate the probability of a bond being on the infinite cluster and also on the overconstrained part of the infinite cluster, and show how a specific heat can be defined as the second derivative of the free energy. We demonstrate that the Bethe lattice solution is equivalent to that of the random bond model, where points are joined randomly (with equal probability at all length scales) to have a given coordination, and then subsequently bonds are randomly removed.Comment: RevTeX 11 pages + epsfig embedded figures. Submitted to Phys. Rev.

Sediment Sorting and Rounding in a Basaltic Glacio-Fluvio-Aeolian Environment: hrisjkull Glacier, Iceland

Sediments and sedimentary rocks preserve a rich history of environment and climate. Identifying these signals requires an understanding of the physical and chemical processes that have affected sedimentary deposits [1]. Such processes include sorting and rounding during transport and chemical alteration through weathering and diagenesis. Although these processes have long been studied in quartz-dominated sedimentary systems [2], a lack of studies of basaltic sedimentary systems limits our interpretations of the environment and climate where mafic source rocks dominate, such as on Mars [3,4]. As part of the SAND-E: Semi-Autonomous Navigation for Detrital Environments project [5], which uses robotic operations to examine physical and chemical changes to sediments in basaltic glacio-fluvialaeolian environments, this research studies changes in sorting and rounding of fluvial-aeolian sediments along a glacier-proximal-to-glacier-distal transect in the outwash-plain of the risjkull glacier in SW Iceland (Fig. 1

Using XRD to Characterize Sediment Sorting in a Mars Analog Glacio-Fluvio-Eolian Basaltic Sedimentary System in Iceland

The martian surface has a primarily basaltic composition and is dominated by sedimentary deposits. Ancient layered sedimentary rocks have been identified across the planet from orbit, have been studied in situ by the Mars Exploration Rovers and the Mars Science Laboratory rover, and will be studied by the Mars 2020 rover. These ancient sedimentary rocks were deposited in fluvial, lacustrine, and eolian environments during a warmer and wetter era on Mars. It is important to study the composition of sediments in Mars analog environments to characterize how minerals in basaltic sedimentary systems are sorted and/or aqueously altered. This information can help us better interpret sedimentary processes from similar deposits on Mars and derive information about the igneous source rocks. Sediment sorting has been studied extensively on Earth, but not typically in basaltic environments. Previous work has addressed sorting of basaltic sediments through experimental techniques and in modern eolian basaltic systems and aqueous alteration in subglacial and proglacial environments. We add to this body of research by studying sediment sorting and aqueous alteration in a glacio-fluvio-eolian basaltic system in southwest Iceland

Overview and Initial Results of SAND-E: Semi-Autonomous Navigation for Detrital Environments

Unmanned aerial systems (UAS) and automated terrain analysis for science and navigation are new technologies for planetary exploration. The Mars Helicopter will fly with the Mars2020 rover, the Dragonfly quadcopter will explore Titan, and Soil Properties and Object Classification (SPOC) software will be used for path planning and navigation on the Mars2020 rover. Using an Argo J5 rover instrumented with stereo cameras and Autonomous Soil Assessment System (ASAS) software, and an off the shelf quadcopter, SAND-E tested the use of automated terrain analysis and UAS data for science operations in a Mars-analog environment in Iceland during July of 2019. Scientifically, we sought to determine changes in the physical and chemical properties of sediments along a glacial-fluvial-aeolian transport pathway. Operationally, we tested rover mission-like scenarios that included UAS images and classified terrain images. Here, we present the initial results for both the operations and science elements of the study. Site Selection: A goal of SAND-E is examine sorting and alteration of sediments in fluvial and aeolian environments in both mineral-dominated and glass-dominated basaltic settings. During the first year of the project we focused on a mineral-dominated environment. Selection of the location was based on prior publications that indicated our selected region had a greater abundance of crystalline sediments than other areas fluvial-aeolian settings in Iceland. Other criteria included the presence of both fluvial and aeolian landforms along a transport pathway such that the sediments in transport could be linked to their source rocks. We chose the Skjaldbreidauhraun glacial outwash plain, which sits at the base of Thrisjkull glacier. The site is 30 km north of Thingvellir National Park and ~2 hours from Reykjavik. The outwash plain is fed by two small catchments that drain from the base of the glacier and cut through hyaloclastite and shield volcano bedrock. The drainage progresses from steep alluvial fans near the glacier into a low-sloping fluvial braidplain that becomes confined by the Skjaldbreidur shield volcano and creates a shallow canyon cut into lava bedrock. The fluvial system was a typical braided alluvial environment composed pebble- and cobble-bedded longitudinal bars and sandy channel beds. The river remained active and fluctuated in response to diurnal runoff cycles near the glacier before disappearing into the sandy substrate downstream. The high concentration of suspended sediment in the river was evident by the cloudy water and the silt and clay-sized sediments that draped the channel beds after abandonment and created playas in the lowest sloping areas of the catchment. The entire fluvial system was affected by the winds generated by frontal systems and katabatic flows descending the glacier. This resulted in the formation of aeolian lag deposits and a wind-deflation plain where the fluvial system was not active. Wind ripples and drifts formed in abandoned fluvial channels from aeolian reworking of the sand-sized fluvial sediments. The silt- and clay-sized sediments found in fluvial channels, bar tops, and playas generated dust plumes during high wind events. Our operation sought to capture the variability in this system by sampling from the range of fluvial and aeolian features 6.3 km (proximal), 11.3 km (medial), and 14.4 km (distal) along the river from its origin at the base of glacier

Atomistic modeling of amorphous silicon carbide: An approximate first-principles study in constrained solution space

Localized basis ab initio molecular dynamics simulation within the density functional framework has been used to generate realistic configurations of amorphous silicon carbide (a-SiC). Our approach consists of constructing a set of smart initial configurations that conform essential geometrical and structural aspects of the materials obtained from experimental data, which is subsequently driven via first-principles force-field to obtain the best solution in a reduced solution space. A combination of a priori information (primarily structural and topological) along with the ab-initio optimization of the total energy makes it possible to model large system size (1000 atoms) without compromising the quantum mechanical accuracy of the force-field to describe the complex bonding chemistry of Si and C. The structural, electronic and the vibrational properties of the models have been studied and compared to existing theoretical models and available data from experiments. We demonstrate that the approach is capable of producing large, realistic configurations of a-SiC from first-principles simulation that display excellent structural and electronic properties of a-SiC. Our study reveals the presence of predominant short-range order in the material originating from heteronuclear Si-C bonds with coordination defect concentration as small as 5% and the chemical disorder parameter of about 8%.Comment: 16 pages, 7 figure