75 research outputs found
Phase coexistence of cluster crystals: beyond the Gibbs phase rule
We report a study of the phase behavior of multiple-occupancy crystals
through simulation. We argue that in order to reproduce the equilibrium
behavior of such crystals it is essential to treat the number of lattice sites
as a constraining thermodynamic variable. The resulting free-energy
calculations thus differ considerably from schemes used for single-occupancy
lattices. Using our approach, we obtain the phase diagram and the bulk modulus
for a generalized exponential model that forms cluster crystals at high
densities. We compare the simulation results with existing theoretical
predictions. We also identify two types of density fluctuations that can lead
to two sound modes and evaluate the corresponding elastic constants.Comment: 4 pages, 3 figure
Lane-formation vs. cluster-formation in two dimensional square-shoulder systems: A genetic algorithm approach
Introducing genetic algorithms as a reliable and efficient tool to find
ordered equilibrium structures, we predict minimum energy configurations of the
square shoulder system for different values of corona width . Varying
systematically the pressure for different values of we obtain
complete sequences of minimum energy configurations which provide a deeper
understanding of the system's strategies to arrange particles in an
energetically optimized fashion, leading to the competing self-assembly
scenarios of cluster-formation vs. lane-formation.Comment: 5 pages, 6 figure
On the thermodynamic properties of the generalized Gaussian core model
We present results of a systematic investigation of the properties of the
generalized Gaussian core model of index n. The potential of this system
interpolates via the index n between the potential of the Gaussian core
model and the penetrable sphere system, thereby varying the steepness
of the repulsion. We have used both conventional and self-consistent liquid
state theories to calculate the structural and thermodynamic properties of
the system; reference data are provided by computer simulations. The results
indicate that the concept of self-consistency becomes indispensable
to guarantee excellent agreement with simulation data; in particular, structural
consistency (in our approach taken into account via the zero separation
theorem) is obviously a very important requirement. Simulation results
for the dimensionless equation of state, βP/%, indicate that for an indexvalue
of 4 a clustering transition, possibly into a structurally ordered phase
might set in as the system is compressed.Ми представляємо результати системного дослідження властивостей узагальненої моделі гаусового кора з індексом n. Потенціал такої системи з допомогою індексу n, що визначає крутизну притягання, дозволяє інтерполювати взаємодії від моделі гаусового кора до системи проникних сфер. Для розрахунку структурних і термодинамічних властивостей нами використовувалися як традиційні, так і самоузгоджені версії теорії рідкого стану, а система відліку бралася з комп’ютерного експерименту. Результати показують, що для отримання доброго узгодження з даними моделювання концепція самоузгодження стає обов’язковою; зокрема структурне узгодження, яке у нашому підході проводиться через теорему нульового розділення, є надзвичайно важливою вимогою. Результати моделювання для обезрозміреного рівняння стану, βP/%, вказують на те, що для моделі з індексом 4 може виникати структурно впорядкована фаза (перехід кластерування) при стисканні системи
Why do ultrasoft repulsive particles cluster and crystallize? Analytical results from density functional theory
We demonstrate the accuracy of the hypernetted chain closure and of the
mean-field approximation for the calculation of the fluid-state properties of
systems interacting by means of bounded and positive-definite pair potentials
with oscillating Fourier transforms. Subsequently, we prove the validity of a
bilinear, random-phase density functional for arbitrary inhomogeneous phases of
the same systems. On the basis of this functional, we calculate analytically
the freezing parameters of the latter. We demonstrate explicitly that the
stable crystals feature a lattice constant that is independent of density and
whose value is dictated by the position of the negative minimum of the Fourier
transform of the pair potential. This property is equivalent with the existence
of clusters, whose population scales proportionally to the density. We
establish that regardless of the form of the interaction potential and of the
location on the freezing line, all cluster crystals have a universal Lindemann
ratio L = 0.189 at freezing. We further make an explicit link between the
aforementioned density functional and the harmonic theory of crystals. This
allows us to establish an equivalence between the emergence of clusters and the
existence of negative Fourier components of the interaction potential. Finally,
we make a connection between the class of models at hand and the system of
infinite-dimensional hard spheres, when the limits of interaction steepness and
space dimension are both taken to infinity in a particularly described fashion.Comment: 19 pages, 5 figures, submitted to J. Chem. Phys; new version: minor
changes in structure of pape
Generation of defects and disorder from deeply quenching a liquid to form a solid
We show how deeply quenching a liquid to temperatures where it is linearly
unstable and the crystal is the equilibrium phase often produces crystalline
structures with defects and disorder. As the solid phase advances into the
liquid phase, the modulations in the density distribution created behind the
advancing solidification front do not necessarily have a wavelength that is the
same as the equilibrium crystal lattice spacing. This is because in a deep
enough quench the front propagation is governed by linear processes, but the
crystal lattice spacing is determined by nonlinear terms. The wavelength
mismatch can result in significant disorder behind the front that may or may
not persist in the latter stage dynamics. We support these observations by
presenting results from dynamical density functional theory calculations for
simple one- and two-component two-dimensional systems of soft core particles.Comment: 25 pages, 11 figure
Synthesis and Quantitative Structure–Activity Relationship of Imidazotetrazine Prodrugs with Activity Independent of O6-Methylguanine-DNA-methyltransferase, DNA Mismatch Repair and p53.
The antitumor prodrug Temozolomide is compromised by its dependence for activity on DNA mismatch repair (MMR) and the repair of the chemosensitive DNA lesion, O6-methylguanine (O6-MeG), by O6-methylguanine-DNA-methyltransferase (EC 2.1.1.63, MGMT). Tumor response is also dependent on wild-type p53. Novel 3-(2-anilinoethyl)-substituted imidazotetrazines are reported that have activity independent of MGMT, MMR and p53. This is achieved through a switch of mechanism so that bioactivity derives from imidazotetrazine-generated arylaziridinium ions that principally modify guanine-N7 sites on DNA. Mono- and bi-functional analogs are reported and a quantitative structure-activity relationship (QSAR) study identified the p-tolyl-substituted bi-functional congener as optimized for potency, MGMT-independence and MMR-independence. NCI60 data show the tumor cell response is distinct from other imidazotetrazines and DNA-guanine-N7 active agents such as nitrogen mustards and cisplatin. The new imidazotetrazine compounds are promising agents for further development and their improved in vitro activity validates the principles on which they were designed
Diversification and Specialization of Plant RBR Ubiquitin Ligases
Background: RBR ubiquitin ligases are components of the ubiquitin-proteasome system present in all eukaryotes. They are characterized by having the RBR (RING – IBR – RING) supradomain. In this study, the patterns of emergence of RBR genes in plants are described. Methodology/Principal Findings: Phylogenetic and structural data confirm that just four RBR subfamilies (Ariadne, ARA54, Plant I/Helicase and Plant II) exist in viridiplantae. All of them originated before the split that separated green algae from the rest of plants. Multiple genes of two of these subfamilies (Ariadne and Plant II) appeared in early plant evolution. It is deduced that the common ancestor of all plants contained at least five RBR genes and the available data suggest that this number has been increasing slowly along streptophyta evolution, although losses, especially of Helicase RBR genes, have also occurred in several lineages. Some higher plants (e. g. Arabidopsis thaliana, Oryza sativa) contain a very large number of RBR genes and many of them were recently generated by tandem duplications. Microarray data indicate that most of these new genes have low-level and sometimes specific expression patterns. On the contrary, and as occurs in animals, a small set of older genes are broadly expressed at higher levels. Conclusions/Significance: The available data suggests that the dynamics of appearance and conservation of RBR genes is quite different in plants from what has been described in animals. In animals, an abrupt emergence of many structurall
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The sub-seasonal to seasonal prediction (S2S) project database
A database containing sub-seasonal to seasonal forecasts from 11 operational centres is available to the research community and will help advance our understanding of the sub-seasonal to seasonal time range.
Demands are growing rapidly in the operational prediction and applications communities for forecasts that fill the gap between medium-range weather and long-range or seasonal forecasts. Based on the potential for improved forecast skill at the sub-seasonal to seasonal time range, a sub-seasonal prediction (S2S) research project has been established by the World Weather Research Program/World Climate Research Program. A main deliverable of this project is the establishment of an extensive database, containing sub-seasonal (up to 60 days) forecasts, 3-weeks behind real-time, and reforecasts from 11 operational centers, modelled in part on the THORPEX Interactive Grand Global Ensemble (TIGGE) database for medium range forecasts (up to 15 days).
The S2S database, available to the research community since May 2015, represents an important tool to advance our understanding of the sub-seasonal to seasonal time range that has been considered for a long time as a “desert of predictability”. In particular, this database will help identify common successes and shortcomings in the model simulation and prediction of sources of sub-seasonal to seasonal predictability. For instance, a preliminary study suggests that the S2S models underestimate significantly the amplitude of the Madden Julian Oscillation (MJO) teleconnections over the Euro-Atlantic sector. The S2S database represents also an important tool for case studies of extreme events. For instance, a multi-model combination of S2S models displays higher probability of a landfall over Vanuatu islands 2 to 3 weeks before tropical cyclone Pam devastated the islands in March 2015
The Progeny of Arabidopsis thaliana Plants Exposed to Salt Exhibit Changes in DNA Methylation, Histone Modifications and Gene Expression
Plants are able to acclimate to new growth conditions on a relatively short time-scale. Recently, we showed that the progeny of plants exposed to various abiotic stresses exhibited changes in genome stability, methylation patterns and stress tolerance. Here, we performed a more detailed analysis of methylation patterns in the progeny of Arabidopsis thaliana (Arabidopsis) plants exposed to 25 and 75 mM sodium chloride. We found that the majority of gene promoters exhibiting changes in methylation were hypermethylated, and this group was overrepresented by regulators of the chromatin structure. The analysis of DNA methylation at gene bodies showed that hypermethylation in the progeny of stressed plants was primarily due to changes in the 5′ and 3′ ends as well as in exons rather than introns. All but one hypermethylated gene tested had lower gene expression. The analysis of histone modifications in the promoters and coding sequences showed that hypermethylation and lower gene expression correlated with the enrichment of H3K9me2 and depletion of H3K9ac histones. Thus, our work demonstrated a high degree of correlation between changes in DNA methylation, histone modifications and gene expression in the progeny of salt-stressed plants
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