Fragment Partitions Research Articles

RNA independent fragment partition method based on deep learning for RNA secondary structure prediction

The non-coding RNA secondary structure largely determines its function. Hence, accuracy in structure acquisition is of great importance. Currently, this acquisition primarily relies on various computational methods. The prediction of the structures of long RNA sequences with high precision and reasonable computational cost remains challenging. Here, we propose a deep learning model, RNA-par, which could partition an RNA sequence into several independent fragments (i-fragments) based on its exterior loops. Each i-fragment secondary structure predicted individually could be further assembled to acquire the complete RNA secondary structure. In the examination of our independent test set, the average length of the predicted i-fragments was 453 nt, which was considerably shorter than that of complete RNA sequences (848 nt). The accuracy of the assembled structures was higher than that of the structures predicted directly using the state-of-the-art RNA secondary structure prediction methods. This proposed model could serve as a preprocessing step for RNA secondary structure prediction for enhancing the predictive performance (especially for long RNA sequences) and reducing the computational cost. In the future, predicting the secondary structure of long-sequence RNA with high accuracy can be enabled by developing a framework combining RNA-par with various existing RNA secondary structure prediction algorithms. Our models, test codes and test data are provided at https://github.com/mianfei71/RNAPar.

EMT: Elegantly Measured Tanner for Key-Value Store on SSD

With the emergence of big data era, NoSQL key-value database is considered as a promising candidate for replacing relational database management system (RDBMS). As cost per GB of flash memory is getting closer to HDD, high performance solid state drive (SSD) is regarded as the best substitute of HDD. However, there are still some issues that need to be taken into consideration. <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">et al.</i> have reported that applying key-value store to SSD with conventional FTL would incur internal fragmentation and further cause the degradation of device lifespan. Although they proposed KVFTL to deal with the above issues, their work gave rise to the read amplification problem. In this article, we investigate the root cause of the read amplification problem and propose elegantly measured tanner FTL (EMT-FTL) to mitigate internal fragmentation and read amplification with acceptable memory overhead. Different from KVFTL that slices a variable-sized value into multiple partitions (up to 20) of different sizes and manages them as a linked chain, EMT-FTL slices a value into 16 KiB full partitions with its remaining bytes treated as a fragment partition and appended to the fragment buffer. For a 64 GiB SSD with 16 KiB pages, the overall memory usage of EMT-FTL is only 8.81% of KVFTL. The experiments showed that EMT-FTL achieved almost the optimal space utilization as KVFTL did under most of traces and averagely improved the <monospace xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">get</monospace> performance by 78.57% (compared with KVFTL) under the traces with request sizes ranging from 1 byte to 16 KiB.

Potential energy surfaces of Polonium isotopes

The evolution of the potential energy landscape is analysed in detail for ten even–even polonium isotopes in the mass range as obtained within the macroscopic–microscopic approach, relying on the Lublin–Strasbourg drop model and the Yukawa-folded single-particle energies for calculating the microscopic shell and pairing corrections. A variant of the modified Funny–Hills nuclear shape parametrization is used to efficiently map possible fission paths. The approach explains the main features of the fragment partition as measured in low-energy fission along the polonium chain. The latter lies in a transitional region of the nuclear chart, and will be essential to consistently understand the evolution of fission properties from neutron-deficient mercury to heavy actinides. The ability of our method to predict fission observables over such an extended region looks promising.

New Scalings in Nuclear Fragmentation

Fragment partitions of fragmenting hot nuclei produced in central and semiperipheral collisions have been compared in the excitation energy region 4-10MeV per nucleon where radial collective expansion takes place. It is shown that, for a given total excitation energy per nucleon, the amount of radial collective energy fixes the mean fragment multiplicity. It is also shown that, at a given total excitation energy per nucleon, the different properties of fragment partitions are completely determined by the reduced fragment multiplicity (i.e., normalized to the source size). Freeze-out volumes seem to play a role in the scalings observed.

Multifragmentation and phase transition for hot nuclei: recent progress

Recent important progress on the knowledge of multifragmentation and phase transition for hot nuclei, thanks to the high detection quality of the INDRA array, is reported. It concerns i) the radial collective energies involved in hot fragmenting nuclei/sources produced in central and semi-peripheral collisions and their influence on the observed fragment partitions, ii) a better knowledge of freeze-out properties obtained by means of a simulation based on all the available experimental information and iii) the quantitative study of the bimodal behaviour of the heaviest fragment distribution for fragmenting hot heavy quasi-projectiles which allows the extraction, for the first time, of an estimate of the latent heat of the phase transition.

Two and three fragment decay from Z = 120 isotopes

The decay into two and three fragments from superheavy nuclei is studied using the macroscopic–microscopic method to obtain the total deformation energy. The two-center shell model is employed to calculate the level scheme transition from the superheavy parent nucleus to the emitted cluster plus daughter nucleus. The three-center shell model is also used to compute the transition toward three equal fragment partition. The levels are used to compute the shell corrections with the Strutinsky method. The liquid drop part is calculated using the Yukawa-plus-exponential model. The total deformation energy is then minimized over a multidimensional space of deformation. The dynamics is completed with the Werner–Wheeler tensor of inertia calculation, and cluster emission paths for binary and ternary splitting are obtained for Z= 120 isotopes.

BINARY AND TERNARY EMISSION FROM SUPERHEAVY NUCLEI

The two center shell model is used to calculate the level scheme transition from the superheavy parent nucleus to the emitted cluster plus the daughter nucleus. The three center shell model is also employed to compute the transition toward eventual three equal fragment partition from the superheavy nuclei. The levels are used to compute the shell corrections within the Strutinsky method. The liquid drop part is calculated using the Yukawa-plus-exponential model. The total deformation energy is then minimized over a multidimensional space of deformation. Dynamics is completed with the Werner-Wheeler tensor calculation, and cluster emission paths for binary and ternary splitting is obtained for Z = 120 isotopes.

On the application of the counterpoise correction for the basis set superposition error in geometry optimization calculations of molecular systems: some inconsistent results

It is shown that the conjecture that the total energy for a given molecular or supermolecular system is affected by basis set superposition error (BSSE) leads to inconsistent results. While the calculations of interaction energies, dissociation energies, or energy barriers depend on the fragments (reactants, products) involved in their definitions and, consequently, are affected by BSSE, the total energies of molecular or supermolecular systems do not depend on any virtual fragment partition and are, therefore, BSSE free.

Many-fragment correlations and possible signature of spinodal fragmentation

Abnormal production of events with almost equal-sized fragments was theoretically proposed as a signature of spinodal instabilities responsible for nuclear multifragmentation. Many-fragment correlations can be used to enlighten any extra production of events with specific fragment partitions. The high sensitivity of such correlation methods makes it particularly appropriate to look for small numbers of events as those expected to have kept a memory of spinodal decomposition properties and to reveal the dynamics of a first-order phase transition for nuclear matter and nuclei. This paper summarizes results obtained so far for both experimental and dynamical simulations data.

Tracking energy fluctuations from fragment partitions in the lattice gas model

Partial energy fluctuations are known tools to reconstruct microcanonical heat capacities. For experimental applications, approximations have been developed to infer fluctuations at freeze out from the observed fragment partitions. The accuracy of this procedure as well as the underlying independent fragment approximation is under debate already at the level of equilibrated systems. Using a well controlled computer experiment, the Lattice Gas model, we critically discuss the thermodynamic conditions under which fragment partitions can be used to reconstruct the thermodynamics of an equilibrated system.

Sequence length variation, indel costs, and congruence in sensitivity analysis.

The behavior of two topological and four character-based congruence measures was explored using different indel treatments in three empirical data sets, each with different alignment difficulties. The analyses were done using direct optimization within a sensitivity analysis framework in which the cost of indels was varied. Indels were treated either as a fifth character state, or strings of contiguous gaps were considered single events by using linear affine gap cost. Congruence consistently improved when indels were treated as single events, but no congruence measure appeared as the obviously preferable one. However, when combining enough data, all congruence measures clearly tended to select the same alignment cost set as the optimal one. Disagreement among congruence measures was mostly caused by a dominant fragment or a data partition that included all or most of the length variation in the data set. Dominance was easily detected, as the character-based congruence measures approached their optimal value when indel costs were incremented. Dominance of a fragment or data partition was overwhelmed when new sequence length-variable fragments or data partitions were added.

Fragmentation path of excited nuclear systems

We perform a study of the fragmentation path of excited nuclear sources, within the framework of a stochastic mean-field approach. We consider the reaction 129Xe + 119Sn at two beam energies: 32 and 50 MeV/ A, for central collisions. It is observed that, after the compression phase the system expands towards a dilute configuration from which it may recontract or evolve into a bubble-like structure. Then fragments are formed through the development of volume and/or surface instabilities. The two possibilities co-exist at 32 MeV/ A, leading to quite different fragment partitions, while at 50 MeV/ A the hollow configuration is observed in all events. Large variances are recovered in a way fully consistent with the presence of spinodal decomposition remnants. Kinematical properties of fragments are discussed and suggested as observables very sensitive to the dominant fragment production mechanism. A larger radial collective flow is observed at 50 MeV/ A, in agreement with experiments.

Heavy residues with A

The cross sections and velocity distributions of heavy residues from the reaction of 20 A MeV 124Sn+ 27Al have been measured at forward angles using the MARS recoil separator at Texas A&M in a wide mass range. A consistent overall description of the measured cross sections and velocity distributions was achieved using a model calculation employing the concept of deep-inelastic transfer for the primary stage of peripheral collisions, pre-equilibrium emission and incomplete fusion for the primary stage of more violent central collisions and the statistical model of multifragmentation (SMM code) for the deexcitation stage. An alternative calculation employing the sequential binary decay (GEMINI code) could not reproduce the observed yields of the residues from violent collisions ( A<90) due to different kinematic properties. The success of SMM demonstrates that the heavy residues originate from events where a competition of thermally equilibrated fragment partitions takes place rather than a sequence of binary decays.

Negative heat capacity in the critical region of nuclear fragmentation: an experimental evidence of the liquid-gas phase transition

An experimental indication of negative heat capacity in excited nuclear systems is inferred from the event by event study of energy fluctuations in Au quasi-projectile sources formed in Au+Au collisions at 35 A.MeV. Equilibrated events are selected and the excited source configuration is reconstructed through a calorimetric analysis of its de-excitation products. Fragment partitions show signs of a critical behavior at about 4.5 A.MeV excitation energy. Around this value the heat capacity shows a negative branch providing a direct evidence of a first order liquid gas phase transition.

Reevaluation of Phylogeny in the Drosophila obscura Species Group Based on Combined Analysis of Nucleotide Sequences

The Drosophila obscura species group has served as an important model system in many evolutionary and population genetic studies. Despite the amount of study this group has received, some phylogenetic relationships remain unclear. While individual analysis of different nuclear, mitochondrial, allozyme, restriction fragment, and morphological data partitions are able to discern relationships among closely related species, they are unable to resolve relationships among the five obscura species subgroups. A combined analysis of several nucleotide data sets is able to provide resolution and support for some nodes not seen or well supported in analyses of individual loci. A phylogeny of the obscura species group based on combined analysis of nucleotide sequences from six mitochondrial and five nuclear loci is presented here. The results of several different combined analyses indicate that the Old World obscura and subobscura subgroups form a monophyletic clade, although they are unable to resolve the relationships among the major lineages within the obscura species group.

Study of multifragmentation patterns induced by spinodal instabilities

In this article we study the characteristics of multifragmentation patterns induced by spinodal instabilities using a stochastic mean-field approach. For two-dimensional unstable nuclear matter, we find that the early fragmentation process occurs accordingly to few dominant unstable wave-lengths. This favours the partition of the system in close-mass pieces, with a lack of very small fragments. Then, we consider the realistic case of spherical systems initialized at low density. The role of finite-size effects, final-state interaction and secondary decay is carefully investigated. We discuss under which conditions some memory of the first dynamical stage survives in the final fragment partitions.

Role of lipid/water partitioning and membrane composition in the uptake of organochlorine pesticides into a freshwater mussel

The aim of this investigation is to understand the factors influencing uptake of persistent organochlorine pesticides into a freshwater mussel ( Sphaerium corneum). Previous work has shown that although a substantial proportion of dieldrin is bound to particulates in the river system, uptake is from the dieldrin in solution. This suggests partitioning of the hydrophobic xenobiotics into membranes as the major route of entry. Membrane composition was established using lipid fractionation into neutral lipids and phospholipids followed by derivatisation to fatty acid methyl esters and estimation using GC/FID. Membrane composition varied with acclimation temperature over the range 5–20°C. Dieldrin concentrations in the mussel at equilibrium with 2000 ng dieldrin/litre water burden were studied at one temperature under laboratory conditions using animals acclimated to different temperatures. Any differences may be explicable in terms of effects of membrane composition on partitioning or other physiological adaptations. To establish which of these factors is most significant a membrane fragment partition system has been analysed in vitro. Preliminary results indicate that although water/lipid partitioning may be important in entry (and exit) of non-polar xenobiotics, significant differences could not be found using current methods. The role of membrane composition and therefore temperature history of the organism may still be significant. The implications of this for attempted correlations between bioaccumulation factors and simple octanol/water partition coefficients are discussed.