Stochastic dynamics of coarse-grained quantum fields in the inflationary universe

AbstractAdvances of single-cell technologies allow scrutinizing of heterogeneous cell states, however, analyzing transitions from snap-shot single-cell transcriptome data remains challenging. To investigate cells with transient properties or mixed identities, we present MuTrans, a method based on multiscale reduction technique for the underlying stochastic dynamical systems that prescribes cell-fate transitions. By iteratively unifying transition dynamics across multiple scales, MuTrans constructs the cell-fate dynamical manifold that depicts progression of cell-state transition, and distinguishes meta-stable and transition cells. In addition, MuTrans quantifies the likelihood of all possible transition trajectories between cell states using the coarse-grained transition path theory. Downstream analysis identifies distinct genes that mark the transient states or drive the transitions. Mathematical analysis reveals consistency of the method with the well-established Langevin equation and transition rate theory. Applying MuTrans to datasets collected from five different single-cell experimental platforms and benchmarking with seven existing tools, we show its capability and scalability to robustly unravel complex cell fate dynamics induced by transition cells in systems such as tumor EMT, iPSC differentiation and blood cell differentiation. Overall, our method bridges data-driven and model-based approaches on cell-fate transitions at single-cell resolution.

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STOCHASTIC DYNAMICS OF SCALAR FIELD IN THE INFLATIONARY UNIVERSE

International Journal of Modern Physics A ◽

10.1142/s0217751x89001011 ◽

1989 ◽

Vol 04 (10) ◽

pp. 2613-2625 ◽

Cited By ~ 17

Author(s):

AKIO HOSOYA ◽

MASAHIRO MORIKAWA ◽

KEIJI NAKAYAMA

Keyword(s):

Langevin Equation ◽

Stochastic Dynamics ◽

Momentum Tensor ◽

Inflationary Universe ◽

De Sitter ◽

Tensor Correlation ◽

Long Wavelength ◽

Statistical Correlations ◽

Effective Dynamics ◽

Density Perturbations

An effective dynamics of a long wavelength part of an inflation in de Sitter space is derived in the form of the Langevin equation by regarding the remaining short wavelength part as a noise. Classical properties of the noise and the long wavelength part are investigated and their statistical correlations are derived. The formulation is applied to the generation of density perturbations. Here the interaction in the Langevin equation is shown to be indispensable as far as we disregard the singular contribution of the energy-momentum tensor correlation.

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Large-scale simulation of biomembranes: bringing realistic kinetics to coarse-grained models

10.1101/815571 ◽

2019 ◽

Author(s):

Mohsen Sadeghi ◽

Frank Noé

Keyword(s):

Large Scale ◽

Stochastic Dynamics ◽

Computational Cost ◽

Coarse Grained ◽

Fluctuation Spectrum ◽

Biologically Relevant ◽

Membrane Models ◽

Kinetic Effects ◽

The Cost ◽

Low Computational Cost

Biomembranes are two-dimensional assemblies of phospholipids that are only a few nanometres thick, but form micrometer-sized structures vital to cellular function. Explicit modelling of biologically relevant membrane systems is computationally expensive, especially when the large number of solvent particles and slow membrane kinetics are taken into account. While highly coarse-grained solvent-free models are available to study equilibrium behaviour of membranes, their efficiency comes at the cost of sacrificing realistic kinetics, and thereby the ability to predict pathways and mechanisms of membrane processes. Here, we present a framework for integrating coarse-grained membrane models with anisotropic stochastic dynamics and continuum-based hydrodynamics, allowing us to simulate large biomembrane systems with realistic kinetics at low computational cost. This paves the way for whole-cell simulations that still include nanometer/nanosecond spatiotemporal resolutions. As a demonstration, we obtain and verify fluctuation spectrum of a full-sized human red blood cell in a 150-milliseconds-long single trajectory. We show how the kinetic effects of different cytoplasmic viscosities can be studied with such a simulation, with predictions that agree with single-cell experimental observations.

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Dissecting transition cells from single-cell transcriptome data through multiscale stochastic dynamics

Nature Communications ◽

10.1038/s41467-021-25548-w ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Peijie Zhou ◽

Shuxiong Wang ◽

Tiejun Li ◽

Qing Nie

Keyword(s):

Single Cell ◽

Cell Fate ◽

Stochastic Dynamics ◽

Coarse Grained ◽

State Transitions ◽

Rate Theory ◽

Transcriptome Data ◽

Cell State ◽

Cell Transcriptome ◽

Single Cell Transcriptome

AbstractAdvances in single-cell technologies allow scrutinizing of heterogeneous cell states, however, detecting cell-state transitions from snap-shot single-cell transcriptome data remains challenging. To investigate cells with transient properties or mixed identities, we present MuTrans, a method based on multiscale reduction technique to identify the underlying stochastic dynamics that prescribes cell-fate transitions. By iteratively unifying transition dynamics across multiple scales, MuTrans constructs the cell-fate dynamical manifold that depicts progression of cell-state transitions, and distinguishes stable and transition cells. In addition, MuTrans quantifies the likelihood of all possible transition trajectories between cell states using coarse-grained transition path theory. Downstream analysis identifies distinct genes that mark the transient states or drive the transitions. The method is consistent with the well-established Langevin equation and transition rate theory. Applying MuTrans to datasets collected from five different single-cell experimental platforms, we show its capability and scalability to robustly unravel complex cell fate dynamics induced by transition cells in systems such as tumor EMT, iPSC differentiation and blood cell differentiation. Overall, our method bridges data-driven and model-based approaches on cell-fate transitions at single-cell resolution.

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The Alteration of the Pore Spaces in Sandstones

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100071491 ◽

1973 ◽

Vol 31 ◽

pp. 210-211

Author(s):

R. E. Ferrell ◽

G. G. Paulson

Keyword(s):

Electron Microscope ◽

Scanning Electron Microscope ◽

The Other ◽

Coarse Grained ◽

Depositional Fabric ◽

Soluble Components ◽

Scanning Electron ◽

Shape And Size

The pore spaces in sandstones are the result of the original depositional fabric and the degree of post-depositional alteration that the rock has experienced. The largest pore volumes are present in coarse-grained, well-sorted materials with high sphericity. The chief mechanisms which alter the shape and size of the pores are precipitation of cementing agents and the dissolution of soluble components. Each process may operate alone or in combination with the other, or there may be several generations of cementation and solution.The scanning electron microscope has ‘been used in this study to reveal the morphology of the pore spaces in a variety of moderate porosity, orthoquartzites.

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On the Origin of the Microscystalline Structure in Rapidly Solidified IN-100 Powder

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100078821 ◽

1977 ◽

Vol 35 ◽

pp. 260-261

Author(s):

J. M. Walsh ◽

K. P. Gumz ◽

J. C. Whittles ◽

B. H. Kear

Keyword(s):

The Other ◽

Coarse Grained ◽

Microcrystalline Structure ◽

Routine Examination ◽

Atomization Process ◽

Centrifugal Atomization ◽

Splat Quenching ◽

Powder Particles ◽

Dendritic Microstructures ◽

Rapidly Solidified

During a routine examination of the microstructure of rapidly solidified IN-100 powder, produced by a newly-developed centrifugal atomization process1, essentially two distinct types of microstructure were identified. When a high melt superheat is maintained during atomization, the powder particles are predominantly coarse-grained, equiaxed or columnar, with distinctly dendritic microstructures, Figs, la and 4a. On the other hand, when the melt superheat is reduced by increasing the heat flow to the disc of the rotary atomizer, the powder particles are predominantly microcrystalline in character, with typically one dendrite per grain, Figs, lb and 4b. In what follows, evidence is presented that strongly supports the view that the unusual microcrystalline structure has its origin in dendrite erosion occurring in a 'mushy zone' of dynamic solidification on the disc of the rotary atomizer.The critical observations were made on atomized material that had undergone 'splat-quenching' on previously solidified, chilled substrate particles.

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Correlation between dislocation, grain boundary and interface of duplex SS in stress corrosion cracking(SCC)

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100177775 ◽

1990 ◽

Vol 48 (4) ◽

pp. 928-929

Author(s):

Wang Zheng-fang ◽

Z.F. Wang

Keyword(s):

Stainless Steel ◽

Thermal Cycle ◽

Secondary Phase ◽

Corrosion Cracking ◽

Coarse Grained ◽

Test Environment ◽

Fine Grained ◽

Evaluation Test ◽

Welding Thermal Cycle ◽

Micro Analysis

The main purpose of this study highlights on the evaluation of chloride SCC resistance of the material,duplex stainless steel,OOCr18Ni5Mo3Si2 (18-5Mo) and its welded coarse grained zone(CGZ).18-5Mo is a dual phases (A+F) stainless steel with yield strength:512N/mm2 .The proportion of secondary Phase(A phase) accounts for 30-35% of the total with fine grained and homogeneously distributed A and F phases(Fig.1).After being welded by a specific welding thermal cycle to the material,i.e. Tmax=1350°C and t8/5=20s,microstructure may change from fine grained morphology to coarse grained morphology and from homogeneously distributed of A phase to a concentration of A phase(Fig.2).Meanwhile,the proportion of A phase reduced from 35% to 5-10°o.For this reason it is known as welded coarse grained zone(CGZ).In association with difference of microstructure between base metal and welded CGZ,so chloride SCC resistance also differ from each other.Test procedures:Constant load tensile test(CLTT) were performed for recording Esce-t curve by which corrosion cracking growth can be described, tf,fractured time,can also be recorded by the test which is taken as a electrochemical behavior and mechanical property for SCC resistance evaluation. Test environment:143°C boiling 42%MgCl2 solution is used.Besides, micro analysis were conducted with light microscopy(LM),SEM,TEM,and Auger energy spectrum(AES) so as to reveal the correlation between the data generated by the CLTT results and micro analysis.

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