CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single-cells

AbstractChromatin interactions are important for gene regulation and cellular specialization. Emerging evidence suggests many-body spatial interactions can play important roles in condensing super-enhancer regions into a cohesive transcriptional apparatus. Chromosome conformation studies using Hi-C are limited to pairwise, population-averaged interactions; therefore, not suitable for direct assessment of many-body interactions. We describe a computational model, CHROMATIX, that reconstructs structural ensembles based on Hi-C data and identifies significant many-body interactions. For a diverse set of highly-active transcriptional loci with at least 2 super-enhancers, we detail the many-body functional landscape and show DNase-accessibility, POLR2A binding, and decreased H3K27me3 are predictive of interaction-enriched regions.

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Revealing the many-body interactions and valley-polarization behavior in Re-doped MoS2 monolayers

Applied Physics Letters ◽

10.1063/5.0045916 ◽

2021 ◽

Vol 118 (11) ◽

pp. 113101

Author(s):

Xiaoli Zhu ◽

Siting Ding ◽

Lihui Li ◽

Ying Jiang ◽

Biyuan Zheng ◽

...

Keyword(s):

Many Body ◽

Polarization Behavior ◽

Valley Polarization ◽

Mos2 Monolayers ◽

The Many ◽

Many Body Interactions

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Dislocation Generation and Crack Propagation in Metals Examined in Molecular Dynamics Simulations

MRS Proceedings ◽

10.1557/proc-278-173 ◽

1992 ◽

Vol 278 ◽

Cited By ~ 6

Author(s):

J. A. Rifkin ◽

C. S. Becquart ◽

D. Kim ◽

P. C. Clapp

Keyword(s):

Crack Propagation ◽

Atomistic Simulations ◽

Many Body ◽

Dislocation Generation ◽

Embedded Atom ◽

Stress Levels ◽

Different Temperatures ◽

The Many ◽

Dynamics Simulations ◽

Many Body Interactions

AbstractWe have carried out a series of atomistic simulations on arrays of about 10,000 atoms containing an atomically sharp crack and subjected to increasing stress levels. The ordered stoichiometric alloys B2 NiAl, B2 RuAl and A15 Nb3AI have been studied at different temperatures and stress levels, as well as the elements Al, Ni, Nb and Ru. The many body interactions used in the simulations were derived semi-empirically, using techniques related to the Embedded Atom Method. Trends in dislocation generation rates and crack propagation modes will be discussed and compared to experimental indications where possible, and some of the simulations will be demonstrated in the form of computer movies.

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Possible weakening of the many-body interactions in the organic quasi-two-dimensional metal α-(BETS)2NH4Hg(SCN)4

Journal of Experimental and Theoretical Physics ◽

10.1134/s1063776109100124 ◽

2009 ◽

Vol 109 (4) ◽

pp. 664-666 ◽

Cited By ~ 4

Author(s):

S. I. Pesotskiĭ ◽

R. B. Lyubovskiĭ ◽

M. V. Kartsovnik ◽

W. Biberacher ◽

N. D. Kushch ◽

...

Keyword(s):

Two Dimensional ◽

Many Body ◽

The Many ◽

Many Body Interactions

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Cliques Are Bricks for k-CT Graphs

Mathematics ◽

10.3390/math9111160 ◽

2021 ◽

Vol 9 (11) ◽

pp. 1160

Author(s):

Václav Snášel ◽

Pavla Dráždilová ◽

Jan Platoš

Keyword(s):

Complex Networks ◽

Simplicial Complex ◽

Dynamic Properties ◽

Simplicial Complexes ◽

Many Body ◽

Chemistry Industry ◽

The Past ◽

Pairwise Interactions ◽

The Many ◽

Many Body Interactions

Many real networks in biology, chemistry, industry, ecological systems, or social networks have an inherent structure of simplicial complexes reflecting many-body interactions. Over the past few decades, a variety of complex systems have been successfully described as networks whose links connect interacting pairs of nodes. Simplicial complexes capture the many-body interactions between two or more nodes and generalized network structures to allow us to go beyond the framework of pairwise interactions. Therefore, to analyze the topological and dynamic properties of simplicial complex networks, the closed trail metric is proposed here. In this article, we focus on the evolution of simplicial complex networks from clicks and k-CT graphs. This approach is used to describe the evolution of real simplicial complex networks. We conclude with a summary of composition k-CT graphs (glued graphs); their closed trail distances are in a specified range.

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Time Dependence of the Many-Body Interactions in a One-Dimensional Sample of Ultracold Rydberg Atoms

Conference on Coherence and Quantum Optics ◽

10.1364/cqo.2007.jwc12 ◽

2007 ◽

Author(s):

Thomas J. Carroll ◽

Cordelia Ochis ◽

Peter D. Maenner ◽

Michael W. Noel

Keyword(s):

Time Dependence ◽

Rydberg Atoms ◽

Many Body ◽

One Dimensional ◽

The Many ◽

Many Body Interactions

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A hybrid model of Skyrme- and Brueckner-type interactions for neutron star matter

Progress of Theoretical and Experimental Physics ◽

10.1093/ptep/ptz139 ◽

2020 ◽

Vol 2020 (1) ◽

Author(s):

Soonchul Choi ◽

Myung-Ki Cheoun ◽

K S Kim ◽

Hungchong Kim ◽

H Sagawa

Keyword(s):

Neutron Star ◽

Hybrid Model ◽

Clear Understanding ◽

Neutron Skin ◽

Neutron Star Matter ◽

Many Body ◽

Hartree Fock ◽

Nuclear Incompressibility ◽

The Many ◽

Many Body Interactions

Abstract We suggest a hybrid model for neutron star matter to discuss the hyperon puzzle inherent in the 2.0 M$_{\odot}$ of the neutron star. For the nucleon–nucleon ($NN$) interaction, we employ the Skyrme–Hartree–Fock approach based on various Skyrme interaction parameter sets, and take the Brueckner–Hartree–Fock approach for the interactions related to hyperons. For the many-body interactions including hyperons, we make use of the multi-pomeron-exchange model, whose parameters have been adjusted to the data deduced from various hypernuclei properties. For clear understanding of the physics in the hybrid model, we discuss fractional functions of related particles, symmetry energies, and chemical potentials in dense matter. Finally, we investigate the equations of state and mass–radius relation of neutron stars, and show that the hybrid model can properly describe the 2.0 M$_{\odot}$ neutron star mass data with the many-body interaction employed in the hybrid model. Recent tidal deformability data from the gravitational wave observation are also compared to our calculations, especially in terms of the neutron skin of $^{208}$Pb and nuclear incompressibility.

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First Principles Calculation of Phase Stability of High Temperature Intermetallic Alloys

MRS Proceedings ◽

10.1557/proc-213-119 ◽

1990 ◽

Vol 213 ◽

Author(s):

J. Mikalopas ◽

P.A. Sterne ◽

M. Sluiter ◽

P.E.A. Turchi

Keyword(s):

First Principles ◽

Strong Dependence ◽

Cluster Variation Method ◽

First Principles Calculation ◽

Variation Method ◽

Many Body ◽

Coherent Phase Diagram ◽

Cluster Variation ◽

The Many ◽

Many Body Interactions

ABSTRACTOne way to calculate the coherent phase diagram of an alloy based on first principles methods is to compute the ground state total energy for various ordered configurations, from which many-body interactions can be calculated and employed in a thermodynamic model. If the Connolly and Williams method (CWM) is used to extract the many-body interactions from the calculated total energies, the resulting many-body interactions can exhibit a strong dependence on the choice of ordered configurations and multi-site clusters, and the accuracy and convergence of the CWM energy expansion is not assured. To overcome this difficulty, a successful systematic method for implementing the CWM is proposed. This approach is applied to a study of the fcc-based Ni-V and Pd-V substitutional alloys and these interaction parameters together with the cluster variation method (CVM) are used to calculate phase diagrams.

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A Review of Many-Body Interactions in Linear and Nonlinear Plasmonic Nanohybrids

Symmetry ◽

10.3390/sym13030445 ◽

2021 ◽

Vol 13 (3) ◽

pp. 445

Author(s):

Mahi R. Singh

Keyword(s):

Metallic Nanoparticles ◽

Dipole Interaction ◽

Many Body ◽

Dipole Coupling ◽

The Many ◽

Two Peaks ◽

Many Body Interactions ◽

Plasmon Polaritons ◽

Strong Dipole ◽

Quantum Emitters

In this review article, we discuss the many-body interactions in plasmonic nanohybrids made of an ensemble of quantum emitters and metallic nanoparticles. A theory of the linear and nonlinear optical emission intensity was developed by using the many-body quantum mechanical density matrix method. The ensemble of quantum emitters and metallic nanoparticles interact with each other via the dipole-dipole interaction. Surfaces plasmon polaritons are located near to the surface of the metallic nanoparticles. We showed that the nonlinear Kerr intensity enhances due to the weak dipole-dipole coupling limits. On the other hand, in the strong dipole-dipole coupling limit, the single peak in the Kerr intensity splits into two peaks. The splitting of the Kerr spectrum is due to the creation of dressed states in the plasmonic nanohybrids within the strong dipole-dipole interaction. Further, we found that the Kerr nonlinearity is also enhanced due to the interaction between the surface plasmon polaritons and excitons of the quantum emitters. Next, we predicted the spontaneous decay rates are enhanced due to the dipole-dipole coupling. The enhancement of the Kerr intensity due to the surface plasmon polaritons can be used to fabricate nanosensors. The splitting of one peak (ON) two peaks (OFF) can be used to fabricate the nanoswitches for nanotechnology and nanomedical applications.

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