Ab initio Molecular Dynamical Investigation of the Finite Temperature Behavior of the Tetrahedral Au19_{19} and Au20_{20} Clusters

Density functional molecular dynamics simulations have been carried out to understand the finite temperature behavior of Au$_{19}$ and Au$_{20}$ clusters. Au$_{20}$ has been reported to be a unique molecule having tetrahedral geometry, a large HOMO-LUMO energy gap and an atomic packing similar to that of the bulk gold (J. Li et al., Science, {\bf 299} 864, 2003). Our results show that the geometry of Au$_{19}$ is exactly identical to that of Au$_{20}$ with one missing corner atom (called as vacancy). Surprisingly, our calculated heat capacities for this nearly identical pair of gold cluster exhibit dramatic differences. Au$_{20}$ undergoes a clear and distinct solid like to liquid like transition with a sharp peak in the heat capacity curve around 770 K. On the other hand, Au$_{19}$ has a broad and flat heat capacity curve with continuous melting transition. This continuous melting transition turns out to be a consequence of a process involving series of atomic rearrangements along the surface to fill in the missing corner atom. This results in a restricted diffusive motion of atoms along the surface of Au$_{19}$ between 650 K to 900 K during which the shape of the ground state geometry is retained. In contrast, the tetrahedral structure of Au$_{20}$ is destroyed around 800 K, and the cluster is clearly in a liquid like state above 1000 K. Thus, this work clearly demonstrates that (i) the gold clusters exhibit size sensitive variations in the heat capacity curves and (ii) the broad and continuous melting transition in a cluster, a feature which has so far been attributed to the disorder or absence of symmetry in the system, can also be a consequence of a defect (absence of a cap atom) in the structure.Comment: 7 figure

Theory and computation of directional nematic phase ordering

A computational study of morphological instabilities of a two-dimensional nematic front under directional growth was performed using a Landau-de Gennes type quadrupolar tensor order parameter model for the first-order isotropic/nematic transition of 5CB (pentyl-cyanobiphenyl). A previously derived energy balance, taking anisotropy into account, was utilized to account for latent heat and an imposed morphological gradient in the time-dependent model. Simulations were performed using an initially homeotropic isotropic/nematic interface. Thermal instabilities in both the linear and non-linear regimes were observed and compared to past experimental and theoretical observations. A sharp-interface model for the study of linear morphological instabilities, taking into account additional complexity resulting from liquid crystalline order, was derived. Results from the sharp-interface model were compared to those from full two-dimensional simulation identifying the specific limitations of simplified sharp-interface models for this liquid crystal system. In the nonlinear regime, secondary instabilities were observed to result in the formation of defects, interfacial heterogeneities, and bulk texture dynamics.Comment: first revisio

Sign patterns for chemical reaction networks

Most differential equations found in chemical reaction networks (CRNs) have the form $dx/dt=f(x)= Sv(x)$, where $x$ lies in the nonnegative orthant, where $S$ is a real matrix (the stoichiometric matrix) and $v$ is a column vector consisting of real-valued functions having a special relationship to $S$. Our main interest will be in the Jacobian matrix, $f'(x)$, of $f(x)$, in particular in whether or not each entry $f'(x)_{ij}$ has the same sign for all $x$ in the orthant, i.e., the Jacobian respects a sign pattern. In other words species $x_j$ always acts on species $x_i$ in an inhibitory way or its action is always excitatory. In Helton, Klep, Gomez we gave necessary and sufficient conditions on the species-reaction graph naturally associated to $S$ which guarantee that the Jacobian of the associated CRN has a sign pattern. In this paper, given $S$ we give a construction which adds certain rows and columns to $S$, thereby producing a stoichiometric matrix $\widehat S$ corresponding to a new CRN with some added species and reactions. The Jacobian for this CRN based on $\hat S$ has a sign pattern. The equilibria for the $S$ and the $\hat S$ based CRN are in exact one to one correspondence with each equilibrium $e$ for the original CRN gotten from an equilibrium $\hat e$ for the new CRN by removing its added species. In our construction of a new CRN we are allowed to choose rate constants for the added reactions and if we choose them large enough the equilibrium $\hat e$ is locally asymptotically stable if and only if the equilibrium $e$ is locally asymptotically stable. Further properties of the construction are shown, such as those pertaining to conserved quantities and to how the deficiencies of the two CRNs compare.Comment: 23 page

Non-isothermal model for the direct isotropic/smectic-A liquid crystalline transition

An extension to a high-order model for the direct isotropic/smectic-A liquid crystalline phase transition was derived to take into account thermal effects including anisotropic thermal diffusion and latent heat of phase-ordering. Multi-scale multi-transport simulations of the non-isothermal model were compared to isothermal simulation, showing that the presented model extension corrects the standard Landau-de Gennes prediction from constant growth to diffusion-limited growth, under shallow quench/undercooling conditions. Non-isothermal simulations, where meta-stable nematic pre-ordering precedes smectic-A growth, were also conducted and novel non-monotonic phase-transformation kinetics observed.Comment: First revision: 20 pages, 7 figure

CAPSULE: Language and system support for efficient state sharing in distributed stream processing systems

Data stream processing applications are often expressed as data flow graphs, composed of operators connected via streams. This structured representation provides a simple yet powerful paradigm for building large-scale, distributed, high-performance applications. However, there are many tasks that require sharing data across operators, and across operators and the runtime using a less structured mechanism than point-to-point data flows. Examples include updating control variables, sending notifications, collecting metrics, building collective models, etc. In this paper we describe CAPSULE, which fills this gap. CAPSULE is a code generation and runtime framework that offers an easy to use and highly flexible framework for developers to realize shared variables (CAPSULE term for shared state) by specifying a data structure (at the programming-language level), and a few associated configuration parameters that qualify the expected usage scenario. Besides the easy of use and flexibility, CAPSULE offers the following important benefits: (1) Custom Code Generation - CAPSULE makes use of user-specified configuration parameters and information from the runtime to generate shared variable servers that are tailored for the specific usage scenario, (2) Composability - CAPSULE supports deployment time composition of the shared variable servers to achieve desired levels of scalability, performance and fault-tolerance, and (3) Extensibility - CAPSULE provides simple interfaces for extending the CAPSULE framework with more protocols, transports, caching mechanisms, etc. We describe the motivation for CAPSULE and its design, report on its implementation status, and then present experimental results. Copyright © 2012 ACM

Postoperative analgesia in total knee arthroplasty

Total knee arthroplasty is commonly performed in patients with end-stage osteoarthritis or rheumatic knee arthritis to relieve joint pain, increase mobility, and improve quality of life. Despite advances in surgical techniques, postoperative pain management in these types of patients is still deficient. An exhaustive review was performed with the available literature, using the PubMed, ScienceDirect, Scopus and Cochrane databases from 2004 to 2021. The search criteria were formulated to identify reports related to total knee replacement and pain management. Pain after total knee arthroplasty has been shown to involve both peripheral and central pain pathways, which is why various postoperative pain management strategies are currently applied, including patient-controlled analgesia, continuous peripheral nerve blocks, or single injection or local infiltration analgesia. Today local techniques such as periarticular injections are becoming more common in total knee replacement due to their effectiveness in controlling pain without causing muscle weakness. The development of minimally invasive techniques associated with multimodal and preventive analgesia improves recovery rates and early rehabilitation in patients undergoing total knee arthroplasty, reducing in-hospital costs, risk of complications, and improving patient satisfaction with chronic osteoarthropathy.

The Landscape Archaeology of Knettishall Heath, Suffolk and its Implications

This paper briefly describes the results of archaeological fieldwork carried out in an area of heathland, currently managed as a nature reserve, in East Anglia. Although the earthworks recorded are for the most part unremarkable, they demonstrate the variety and intensity of human exploitation which shaped this ‘traditionally managed’ habitat. They also serve to emphasise the extent to which modern conservation management can radically change the long-term character of individual places

Optimizing Reserve Expansion For Disjunct Populations Of San Joaquin Kit Fox

Expanding habitat protection is a common strategy for species conservation. We present a model to optimize the expansion of reserves for disjunct populations of an endangered species. The objective is to maximize the expected number of surviving populations subject to budget and habitat constraints. The model accounts for benefits of reserve expansion in terms of likelihood of persistence of each population and monetary cost. Solving the model with incrementally higher budgets helps prioritize sites for expansion and produces a cost curve showing funds required for incremental increases in the objective. We applied the model to the problem of allocating funds among eight reserves for the endangered San Joaquin kit fox (Vulpes macrotis mutica) in California, USA. The priorities for reserve expansion were related to land cost and amount of already-protected habitat at each site. Western Kern and Ciervo-Panoche sites received highest priority because land costs were low and moderate amounts of already-protected habitat resulted in large reductions in extinction risk for small increments of habitat protection. The sensitivity analysis focused on the impacts of kit fox reproductive success and home range in non-native grassland sites. If grassland habitat is lower quality than brushland habitat resulting in higher annual variation in reproductive success or larger home ranges, then protecting habitat at the best grassland site (Ciervo-Panoche) is not cost–efficient relative to shrubland sites (Western Kern, Antelope Plain, Carrizo Plain). Finally, results suggested that lowest priority should be given to three relatively high-cost grassland sites (Camp Roberts, Contra Costa, and Western Madera) because protecting habitat at those sites would be expensive and have little effect on the expected number of surviving kit fox populations

Computing paths and cycles in biological interaction graphs

<p>Abstract</p> <p>Background</p> <p>Interaction graphs (signed directed graphs) provide an important qualitative modeling approach for Systems Biology. They enable the analysis of causal relationships in cellular networks and can even be useful for predicting qualitative aspects of systems dynamics. Fundamental issues in the analysis of interaction graphs are the enumeration of paths and cycles (feedback loops) and the calculation of shortest positive/negative paths. These computational problems have been discussed only to a minor extent in the context of Systems Biology and in particular the shortest signed paths problem requires algorithmic developments.</p> <p>Results</p> <p>We first review algorithms for the enumeration of paths and cycles and show that these algorithms are superior to a recently proposed enumeration approach based on elementary-modes computation. The main part of this work deals with the computation of shortest positive/negative paths, an NP-complete problem for which only very few algorithms are described in the literature. We propose extensions and several new algorithm variants for computing either exact results or approximations. Benchmarks with various concrete biological networks show that exact results can sometimes be obtained in networks with several hundred nodes. A class of even larger graphs can still be treated exactly by a new algorithm combining exhaustive and simple search strategies. For graphs, where the computation of exact solutions becomes time-consuming or infeasible, we devised an approximative algorithm with polynomial complexity. Strikingly, in realistic networks (where a comparison with exact results was possible) this algorithm delivered results that are very close or equal to the exact values. This phenomenon can probably be attributed to the particular topology of cellular signaling and regulatory networks which contain a relatively low number of negative feedback loops.</p> <p>Conclusion</p> <p>The calculation of shortest positive/negative paths and cycles in interaction graphs is an important method for network analysis in Systems Biology. This contribution draws the attention of the community to this important computational problem and provides a number of new algorithms, partially specifically tailored for biological interaction graphs. All algorithms have been implemented in the <it>CellNetAnalyzer </it>framework which can be downloaded for academic use at <url>http://www.mpi-magdeburg.mpg.de/projects/cna/cna.html</url>.</p