572 research outputs found
CALYPSO: a method for crystal structure prediction
We have developed a software package CALYPSO (Crystal structure AnaLYsis by
Particle Swarm Optimization) to predict the energetically stable/metastable
crystal structures of materials at given chemical compositions and external
conditions (e.g., pressure). The CALYPSO method is based on several major
techniques (e.g. particle-swarm optimization algorithm, symmetry constraints on
structural generation, bond characterization matrix on elimination of similar
structures, partial random structures per generation on enhancing structural
diversity, and penalty function, etc) for global structural minimization from
scratch. All of these techniques have been demonstrated to be critical to the
prediction of global stable structure. We have implemented these techniques
into the CALYPSO code. Testing of the code on many known and unknown systems
shows high efficiency and high successful rate of this CALYPSO method [Wang et
al., Phys. Rev. B 82 (2010) 094116][1]. In this paper, we focus on descriptions
of the implementation of CALYPSO code and why it works.Comment: accepted in Computer Physics Communication
Multilevel Deconstruction of the In Vivo Behavior of Looped DNA-Protein Complexes
Protein-DNA complexes with loops play a fundamental role in a wide variety of
cellular processes, ranging from the regulation of DNA transcription to
telomere maintenance. As ubiquitous as they are, their precise in vivo
properties and their integration into the cellular function still remain
largely unexplored. Here, we present a multilevel approach that efficiently
connects in both directions molecular properties with cell physiology and use
it to characterize the molecular properties of the looped DNA-lac repressor
complex while functioning in vivo. The properties we uncover include the
presence of two representative conformations of the complex, the stabilization
of one conformation by DNA architectural proteins, and precise values of the
underlying twisting elastic constants and bending free energies. Incorporation
of all this molecular information into gene-regulation models reveals an
unprecedented versatility of looped DNA-protein complexes at shaping the
properties of gene expression.Comment: Open Access article available at
http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi%2F10.1371%2Fjournal.pone.000035
Mathematical description of bacterial traveling pulses
The Keller-Segel system has been widely proposed as a model for bacterial
waves driven by chemotactic processes. Current experiments on {\em E. coli}
have shown precise structure of traveling pulses. We present here an
alternative mathematical description of traveling pulses at a macroscopic
scale. This modeling task is complemented with numerical simulations in
accordance with the experimental observations. Our model is derived from an
accurate kinetic description of the mesoscopic run-and-tumble process performed
by bacteria. This model can account for recent experimental observations with
{\em E. coli}. Qualitative agreements include the asymmetry of the pulse and
transition in the collective behaviour (clustered motion versus dispersion). In
addition we can capture quantitatively the main characteristics of the pulse
such as the speed and the relative size of tails. This work opens several
experimental and theoretical perspectives. Coefficients at the macroscopic
level are derived from considerations at the cellular scale. For instance the
stiffness of the signal integration process turns out to have a strong effect
on collective motion. Furthermore the bottom-up scaling allows to perform
preliminary mathematical analysis and write efficient numerical schemes. This
model is intended as a predictive tool for the investigation of bacterial
collective motion
Cyclic Density Functional Theory : A route to the first principles simulation of bending in nanostructures
We formulate and implement Cyclic Density Functional Theory (Cyclic DFT) -- a
self-consistent first principles simulation method for nanostructures with
cyclic symmetries. Using arguments based on Group Representation Theory, we
rigorously demonstrate that the Kohn-Sham eigenvalue problem for such systems
can be reduced to a fundamental domain (or cyclic unit cell) augmented with
cyclic-Bloch boundary conditions. Analogously, the equations of electrostatics
appearing in Kohn-Sham theory can be reduced to the fundamental domain
augmented with cyclic boundary conditions. By making use of this symmetry cell
reduction, we show that the electronic ground-state energy and the
Hellmann-Feynman forces on the atoms can be calculated using quantities defined
over the fundamental domain. We develop a symmetry-adapted finite-difference
discretization scheme to obtain a fully functional numerical realization of the
proposed approach. We verify that our formulation and implementation of Cyclic
DFT is both accurate and efficient through selected examples.
The connection of cyclic symmetries with uniform bending deformations
provides an elegant route to the ab-initio study of bending in nanostructures
using Cyclic DFT. As a demonstration of this capability, we simulate the
uniform bending of a silicene nanoribbon and obtain its energy-curvature
relationship from first principles. A self-consistent ab-initio simulation of
this nature is unprecedented and well outside the scope of any other systematic
first principles method in existence. Our simulations reveal that the bending
stiffness of the silicene nanoribbon is intermediate between that of graphene
and molybdenum disulphide. We describe several future avenues and applications
of Cyclic DFT, including its extension to the study of non-uniform bending
deformations and its possible use in the study of the nanoscale flexoelectric
effect.Comment: Version 3 of the manuscript, Accepted for publication in Journal of
the Mechanics and Physics of Solids,
http://www.sciencedirect.com/science/article/pii/S002250961630368
Community Code Verification Exercise for Simulating Sequences of Earthquakes and Aseismic Slip (SEAS)
Numerical simulations of sequences of earthquakes and aseismic slip (SEAS) have made great progress over past decades to address important questions in earthquake physics. However, significant challenges in SEAS modeling remain in resolving multiscale interactions between earthquake nucleation, dynamic rupture, and aseismic slip, and understanding physical factors controlling observables such as seismicity and ground deformation. The increasing complexity of SEAS modeling calls for extensive efforts to verify codes and advance these simulations with rigor, reproducibility, and broadened impact. In 2018, we initiated a community code‐verification exercise for SEAS simulations, supported by the Southern California Earthquake Center. Here, we report the findings from our first two benchmark problems (BP1 and BP2), designed to verify different computational methods in solving a mathematically well‐defined, basic faulting problem. We consider a 2D antiplane problem, with a 1D planar vertical strike‐slip fault obeying rate‐and‐state friction, embedded in a 2D homogeneous, linear elastic half‐space. Sequences of quasi‐dynamic earthquakes with periodic occurrences (BP1) or bimodal sizes (BP2) and their interactions with aseismic slip are simulated. The comparison of results from 11 groups using different numerical methods show excellent agreements in long‐term and coseismic fault behavior. In BP1, we found that truncated domain boundaries influence interseismic stressing, earthquake recurrence, and coseismic rupture, and that model agreement is only achieved with sufficiently large domain sizes. In BP2, we found that complexity of fault behavior depends on how well physical length scales related to spontaneous nucleation and rupture propagation are resolved. Poor numerical resolution can result in artificial complexity, impacting simulation results that are of potential interest for characterizing seismic hazard such as earthquake size distributions, moment release, and recurrence times. These results inform the development of more advanced SEAS models, contributing to our further understanding of earthquake system dynamics
Dose-Response Aligned Circuits in Signaling Systems
Cells use biological signal transduction pathways to respond to environmental stimuli and the behavior of many cell types depends on precise sensing and transmission of external information. A notable property of signal transduction that was characterized in the Saccharomyces cerevisiae yeast cell and many mammalian cells is the alignment of dose-response curves. It was found that the dose response of the receptor matches closely the dose responses of the downstream. This dose-response alignment (DoRA) renders equal sensitivities and concordant responses in different parts of signaling system and guarantees a faithful information transmission. The experimental observations raise interesting questions about the nature of the information transmission through DoRA signaling networks and design principles of signaling systems with this function. Here, we performed an exhaustive computational analysis on network architectures that underlie the DoRA function in simple regulatory networks composed of two and three enzymes. The minimal circuits capable of DoRA were examined with Michaelis-Menten kinetics. Several motifs that are essential for the dynamical function of DoRA were identified. Systematic analysis of the topology space of robust DoRA circuits revealed that, rather than fine-tuning the network's parameters, the function is primarily realized by enzymatic regulations on the controlled node that are constrained in limiting regions of saturation or linearity
An exceptionally well-preserved skeleton of Palaeothentes from the Early Miocene of Patagonia, Argentina: new insights into the anatomy of extinct paucituberculatan marsupials
International audienc
Interactions between Global Health Initiatives and Country Health Systems: The Case of a Neglected Tropical Diseases Control Program in Mali
Prevention of neglected tropical diseases was recently significantly scaled up in sub-Saharan Africa, protecting entire populations with mass distribution of drugs: five different diseases are now addressed simultaneously with a package of four drugs. Some argue however that, similarly to other major control programs dealing with specific diseases, this NTD campaign fails to strengthen health systems and might even negatively affect regular care provision. In 2007, we conducted an exploratory field study in Mali, observing how the program was implemented in two rural areas and how it affected the health system. At the local level, we found that the campaign effects of care delivery differed across health services. In robust and well staffed health centres, the personnel successfully facilitated mass drug distribution while running routine consultations, and overall service functioning benefitted from programme resources. In more fragile health centres however, additional program workload severely disturbed access to regular care, and we observed operational problems affecting the quality of mass drug distribution. Strong health services appeared to be profitable to the NTD control program as well as to general care
Oscillatory stimuli differentiate adapting circuit topologies
This is the author accepted manuscript. The final version is available from Springer Nature via the DOI in this record.Biology emerges from interactions between molecules, which are challenging to elucidate with current techniques. An orthogonal approach is to probe for 'response signatures' that identify specific circuit motifs. For example, bistability, hysteresis, or irreversibility are used to detect positive feedback loops. For adapting systems, such signatures are not known. Only two circuit motifs generate adaptation: negative feedback loops (NFLs) and incoherent feed-forward loops (IFFLs). On the basis of computational testing and mathematical proofs, we propose differential signatures: in response to oscillatory stimulation, NFLs but not IFFLs show refractory-period stabilization (robustness to changes in stimulus duration) or period skipping. Applying this approach to yeast, we identified the circuit dominating cell cycle timing. In Caenorhabditis elegans AWA neurons, which are crucial for chemotaxis, we uncovered a Ca2+ NFL leading to adaptation that would be difficult to find by other means. These response signatures allow direct access to the outlines of the wiring diagrams of adapting systems.The work was supported by US National Institutes of Health grant 5RO1-GM078153-07 (F.R.C.), NRSA Training Grant CA009673-36A1 (S.J.R.), a Merck Postdoctoral Fellowship at The Rockefeller University (S.J.R.), and the Simons Foundation (S.J.R.). J.L. was supported by a fellowship from the Boehringer Ingelheim Fonds. E.D.S. was partially supported by the US Office of Naval Research (ONR N00014-13-1-0074) and the US Air Force Office of Scientific Research (AFOSR FA9550-14-1-0060)
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