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中国科学院理论物理研究所Thu, 02 Feb 2023 01:25:20 GMT2023-02-02T01:25:20ZProALIGN: Directly Learning Alignments for Protein Structure Prediction via Exploiting Context-Specific Alignment Motifs
http://ir.itp.ac.cn/:80/handle/311006/27911
Title: ProALIGN: Directly Learning Alignments for Protein Structure Prediction via Exploiting Context-Specific Alignment Motifs
Authors: Kong, Lupeng; Ju, Fusong; Zheng, Wei-mou; Zhu, Jianwei; Sun, Shiwei; Xu, Jinbo; Bu, Dongbo
Description: Template-based modeling (TBM), including homology modeling and protein threading, is one of the most reliable techniques for protein structure prediction. It predicts protein structure by building an alignment between the query sequence under prediction and the templates with solved structures. However, it is still very challenging to build the optimal sequence-template alignment, especially when only distantly related templates are available. Here we report a novel deep learning approach ProALIGN that can predict much more accurate sequence-template alignment. Like protein sequences consisting of sequence motifs, protein alignments are also composed of frequently occurring alignment motifs with characteristic patterns. Alignment motifs are context-specific as their characteristic patterns are tightly related to sequence contexts of the aligned regions. Inspired by this observation, we represent a protein alignment as a binary matrix (in which 1 denotes an aligned residue pair) and then use a deep convolutional neural network to predict the optimal alignment from the query protein and its template. The trained neural network implicitly but effectively encodes an alignment scoring function, which reduces inaccuracies in the handcrafted scoring functions widely used by the current threading approaches. For a query protein and a template, we apply the neural network to directly infer likelihoods of all possible residue pairs in their entirety, which could effectively consider the correlations among multiple residues. We further construct the alignment with maximum likelihood, and finally build a structure model according to the alignment. Tested on three independent data sets with a total of 6688 protein alignment targets and 80 CASP13 TBM targets, our method achieved much better alignments and 3D structure models than the existing methods, including HHpred, CNFpred, CEthreader, and DeepThreader. These results clearly demonstrate the effectiveness of exploiting the context-specific alignment motifs by deep learning for protein threading.Mon, 16 Jan 2023 04:57:29 GMThttp://ir.itp.ac.cn/:80/handle/311006/279112023-01-16T04:57:29ZManipulated deformation of lipid bilayer vesicles in magnetic fields
http://ir.itp.ac.cn/:80/handle/311006/27910
Title: Manipulated deformation of lipid bilayer vesicles in magnetic fields
Authors: Shu, Yao-Gen; Ou-Yang, Zhong-Can
Description: We have extended the Helfrich's spontaneous curvature model of the equilibrium vesicle by adding the interaction between magnetic field and the constituent molecules to supply an explaination in principle of the emerging manipulated deformation of a magnetic vesicles such as the reversibly deformation of artificial stomatocyte. The small deformation can be measured by birefringence. Here, we present the derivations of formulas in detailed to reveal the perturbation of deformation $$\psi $$psi under two cases. New features, for example, a 'phase transition' of shape will occur with increasing of $$B$$B from $$B_1<^>*$$B1* to $$B_2<^>*$$B2* for $${\rm \Delta}\chi \lt 0$$& UDelta;chi < 0, in which the major axis of ellipse was rotated by 90 & DEG;, have been revealed. It is worthy for experimenter to demonstrate the 'phase transition'. The significance of imaginary relation ($$B_1<^>* \lt B\lt B_2<^>*$$B1*Mon, 16 Jan 2023 04:57:27 GMThttp://ir.itp.ac.cn/:80/handle/311006/279102023-01-16T04:57:27ZA Machine Learning Model to Classify Dynamic Processes in Liquid Water**
http://ir.itp.ac.cn/:80/handle/311006/27909
Title: A Machine Learning Model to Classify Dynamic Processes in Liquid Water**
Authors: Huang, Jie; Huang, Gang; Li, Shiben
Description: The dynamics of water molecules plays a vital role in understanding water. We combined computer simulation and deep learning to study the dynamics of H-bonds between water molecules. Based on ab initio molecular dynamics simulations and a newly defined directed Hydrogen (H-) bond population operator, we studied a typical dynamic process in bulk water: interchange, in which the H-bond donor reverses roles with the acceptor. By designing a recurrent neural network-based model, we have successfully classified the interchange and breakage processes in water. We have found that the ratio between them is approximately 1 : 4, and it hardly depends on temperatures from 280 to 360 K. This work implies that deep learning has the great potential to help distinguish complex dynamic processes containing H-bonds in other systems.Mon, 16 Jan 2023 04:57:26 GMThttp://ir.itp.ac.cn/:80/handle/311006/279092023-01-16T04:57:26ZLepton number violating electron recoils in a U (1)(B-L) model with non-standard interactions
http://ir.itp.ac.cn/:80/handle/311006/27908
Title: Lepton number violating electron recoils in a U (1)(B-L) model with non-standard interactions
Authors: Lin, Yugen; Gao, Yu; Li, Tianjun
Description: We propose an SU (3)(C) x SU (2)(L) x U (1)(Y) x U(1)(B-L) model, in which the neutrino masses and mix-ings can be generated via Type-I seesaw mechanism after U (1)(B-L) breaking. A light mediator emerges and enables non-standard interaction that violates the lepton number. We show that the non-standard neutrino interaction emerges in this model, and it can lead to low energy recoil events with the solar neutrino flux. Analyses are performed with the keV range electron recoil events at recent direct detection experiments, including XENON1T, PANDAX and XENONnT. Recent direct detection observations lead to upper bound on the combined coupling strength to electron and neutrino to root y(nu)y(e) < 0.5 x 10(-6). (c) 2022 Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). Funded by SCOAP3.Mon, 16 Jan 2023 04:57:24 GMThttp://ir.itp.ac.cn/:80/handle/311006/279082023-01-16T04:57:24ZZigzag magnetic order in a novel tellurate compound Na4-delta NiTeO6 with S=1 chains
http://ir.itp.ac.cn/:80/handle/311006/27907
Title: Zigzag magnetic order in a novel tellurate compound Na4-delta NiTeO6 with S=1 chains
Authors: Su, Cheng; Zeng, Xu-Tao; Li, Yi; Ma, Nvsen; Lin, Zhengwang; Zhang, Chuandi; Wang, Chin-Wei; Chen, Ziyu; Lu, Xingye; Li, Wei; Sheng, Xian-Lei; Jin, Wentao
Description: Na4-delta NiTeO6 is a rare example in the transition-metal tellurate family of realizing an S = 1 spin-chain structure. By performing neutron powder diffraction measurements, the ground-state magnetic structure of Na4-delta NiTeO6 is determined. These measurements reveal that below T-N similar to 6.8(2) K, the Ni2+ moments form a screwed ferromagnetic (FM) spin-chain structure running along the crystallographic a axis but these FM spin chains are coupled antiferromagnetically along the b and c directions, giving rise to a magnetic propagation vector of k = (0, 1/2, 1/2). This zigzag magnetic order is well supported by first-principles calculations. The moment size of Ni2+ spins is determined to be 2.1(1)mu(B) at 3 K, suggesting a significant quenching of the orbital moment due to the crystalline electric field (CEF) effect. The previously reported metamagnetic transition near H-C similar to 0.1 T can be understood as a field-induced spin-flip transition. The relatively easy tunability of the dimensionality of its magnetism by external parameters makes Na4-delta NiTeO6 a promising candidate for further exploring various types of novel spin-chain physics.Mon, 16 Jan 2023 04:57:22 GMThttp://ir.itp.ac.cn/:80/handle/311006/279072023-01-16T04:57:22ZWhen null energy condition meets ADM mass
http://ir.itp.ac.cn/:80/handle/311006/27906
Title: When null energy condition meets ADM mass
Authors: Yang, Run-Qiu; Li, Li; Cai, Rong-Gen
Description: We give a conjecture on the lower bound of the ADM mass M by using the null energy condition. The conjecture includes a Penrose-like inequality 3M >= kA/(4 pi) + root A/4 pi and the Penrose inequality 2M >= root A/4 pi with A the event horizon area and n the surface gravity. Both the conjecture in the static spherically symmetric case and the Penrose inequality for a dynamical spacetime with spherical symmetry are proved by imposing the null energy condition. We then generalize the conjecture to a general dynamical spacetime. Our results raise a new challenge for the famous unsettled question in general relativity: in what general case can the null energy condition replace other energy conditions to ensure the Penrose inequality?Mon, 16 Jan 2023 04:57:21 GMThttp://ir.itp.ac.cn/:80/handle/311006/279062023-01-16T04:57:21ZWhat kind of complexity is dual to holographic complexity?
http://ir.itp.ac.cn/:80/handle/311006/27905
Title: What kind of complexity is dual to holographic complexity?
Authors: Yang, Run-Qiu; An, Yu-Sen; Niu, Chao; Zhang, Cheng-Yong; Kim, Keun-Young
Description: It is assumed that the holographic complexities such as the complexity-action (CA) and the complexity-volume (CV) conjecture are dual to complexity in field theory. However, because the definition of the complexity in field theory is still not complete, the confirmation of the holographic duality of the complexity is ambiguous. To improve this situation, we approach the problem from a different angle. We first identify minimal and genuin properties that the filed theory dual of the holographic complexity should satisfy without assuming anything from the circuit complexity or the information theory. Based on these properties, we propose a field theory formula dual to the holographic complexity. Our field theory formula implies that the complexity between certain states in two dimensional CFTs is given by the Liouville action, which is compatible with the path-integral complexity. It gives natural interpretations for both the CA and CV conjectures and identify what their reference states are. When applied to the thermo-field double states, it also gives consistent results with the holographic results in the CA conjecture: both the divergent term and finite term.Mon, 16 Jan 2023 04:57:20 GMThttp://ir.itp.ac.cn/:80/handle/311006/279052023-01-16T04:57:20ZVan Hove tuning of AV(3)Sb(5) kagome metals under pressure and strain
http://ir.itp.ac.cn/:80/handle/311006/27904
Title: Van Hove tuning of AV(3)Sb(5) kagome metals under pressure and strain
Authors: Consiglio, Armando; Schwemmer, Tilman; Wu, Xianxin; Hanke, Werner; Neupert, Titus; Thomale, Ronny; Sangiovanni, Giorgio; Di Sante, Domenico
Description: From first-principles calculations, we investigate the structural and electronic properties of the kagome metals AV(3)Sb(5) (A = Cs, K, Rb) under isotropic and anisotropic pressure. Charge-ordering patterns are found to be unanimously suppressed, while there is a significant rearrangement of p-type and m-type Van Hove point energies with respect to the Fermi level. Already for moderate tensile strain along the V plane and compressive strain normal to the V layer, we find that a Van Hove point can be shifted to the Fermi energy. Such a mechanism provides an invaluable tuning knob to alter the correlation profile in the kagome metal, and suggests itself for further experimental investigation. It might allow us to reconcile possible multidome superconductivity in kagome metals not only from phonons but also from the viewpoint of unconventional pairing.Mon, 16 Jan 2023 04:57:19 GMThttp://ir.itp.ac.cn/:80/handle/311006/279042023-01-16T04:57:19ZUpdate on strong and radiative decays of the D-s0*(2317) and D-s1(2460) and their bottom cousins
http://ir.itp.ac.cn/:80/handle/311006/27903
Title: Update on strong and radiative decays of the D-s0*(2317) and D-s1(2460) and their bottom cousins
Authors: Fu, Hai-Long; Griesshammer, Harald W.; Guo, Feng-Kun; Hanhart, Christoph; Meissner, Ulf-G
Description: The isospin breaking and radiative decay widths of the positive-parity charm-strange mesons, D-s0* and D-s1, and their predicted bottom-strange counterparts, B-s0* and B-s1, as hadronic molecules are revisited. This is necessary, since the B-s0* and B-s1 masses used in (Cleven et al., Eur Phys J A 50:149, 2014) were too small, in conflict with the heavy quark flavour symmetry. Furthermore, not all isospin breaking contributions were considered. We here present a method to restore heavy quark flavour symmetry, correcting the masses of B-s0* and B-s1, and include the complete isospin breaking contributions up to next-to-leading order. With this we provide updated hadronic decay widths for all of D-s0*, D-s1, B-s0* and B-s1. Results for the partial widths of the radiative deays of D-s0*(2317) and D-s1(2460) are also renewed in light of the much more precisely measured D*(+) width. We find that B-s pi(0) and B-s gamma are the preferred channels for searching for B-s0* and B-s1, respectively.Mon, 16 Jan 2023 04:57:18 GMThttp://ir.itp.ac.cn/:80/handle/311006/279032023-01-16T04:57:18ZUniversal expansions of scattering amplitudes for gravitons, gluons, and Goldstone particles
http://ir.itp.ac.cn/:80/handle/311006/27902
Title: Universal expansions of scattering amplitudes for gravitons, gluons, and Goldstone particles
Authors: Dong, Jin; He, Song; Hou, Linghui
Description: Tree-level scattering amplitudes for gravitons, gluons, and Goldstone particles in any dimensions are strongly constrained by basic principles, and they are intimately related to each other via various relations. We study two types of universal expansions with respect to gauge bosons and Goldstone bosons; the former expresses tree amplitudes in Einstein gravity (Yang-Mills) as linear combinations of single-trace Einstein-Yang-Mills (Yang-Mills-phi(3)) amplitudes with coefficients given by Lorentz products of polarizations and momenta, and the latter expresses tree amplitudes in nonlinear sigma model, (Dirac-)Born-Infeld and a special Galileon theory, as linear combinations of single-trace mixed amplitudes with particles of lower degree of Adler's zero and coefficients given by products of Mandelstam variables. We trace the origin of gauge-theory expansions to the powerful uniqueness theorem based on gauge invariance, and expansions in effective field theories can be derived from gauge-theory ones via a special dimension reduction.Mon, 16 Jan 2023 04:57:17 GMThttp://ir.itp.ac.cn/:80/handle/311006/279022023-01-16T04:57:17Z