scholarly journals FISH-ing for captured contacts: towards reconciling FISH and 3C

2016 ◽  
Author(s):  
Geoff Fudenberg ◽  
Maxim Imakaev
Keyword(s):  
Genomic Sequence ◽  
Three Dimensions ◽  
Spatial Distance ◽  
Chromosome Conformation ◽  
One Dimensional ◽  
Genome Wide ◽  
Contact Frequency ◽  
The One ◽  
Chromosomal Loci

AbstractDeciphering how the one-dimensional information encoded in a genomic sequence is read out in three-dimensions is a pressing contemporary challenge. Chromosome conformation capture (3C) and fluorescence in-situ hybridization (FISH) are two popular technologies that provide important links between genomic sequence and 3D chromosome organization. However, how to integrate views from 3C, or genome-wide Hi-C, and FISH is far from solved. We first discuss what each of these methods measure by reconsidering available matched experimental data for Hi-C and FISH. Using polymer simulations, we then demonstrate that contact frequency is distinct from average spatial distance. We show this distinction can create a seemingly-paradoxical relationship between 3C and FISH. Finally, we consider how the measurement of specific interactions between chromosomal loci might be differentially affected by the two technologies. Together, our results have implications for future attempts to cross-validate and integrate 3C and FISH, as well as for developing models of chromosomes.

Statistical Mechanics of Thermotransport of a Heavy Impurity in an Insulating Solid

1971 ◽  
Vol 26 (1) ◽  
pp. 10-17 ◽  
Author(s):  
A. R. Allnatt
Keyword(s):  
Heat Flux ◽  
Time Correlation ◽  
Three Dimensions ◽  
Time Correlation Functions ◽  
Single Vacancy ◽  
One Dimensional ◽  
Enthalpy Of Activation ◽  
Heavy Impurity ◽  
The One ◽  
Non Equilibrium

AbstractA kinetic equation is derived for the singlet distribution function for a heavy impurity in a lattice of lighter atoms in a temperature gradient. In the one dimensional case the equation can be solved to find formal expressions for the jump probability and hence the heat of transport, q*. for a single vacancy jump of the impurity, q* is the sum of the enthalpy of activation, a term involving only averaging in an equilibrium ensemble, and two non-equilibrium terms in­volving time correlation functions. The most important non-equilibrium term concerns the cor­relation between the force on the impurity and a microscopic heat flux. A plausible extension to three dimensions is suggested and the relation to earlier isothermal and non-isothermal theories is indicated

scholarly journals Hydraulic modeling of combined sewers overflow integrating the results of the SWMM and CFX models.

2021 ◽  
Vol 37 (1) ◽  
Author(s):  
D. Pulgarín ◽  
J. Plaza ◽  
J. Ruge ◽  
J. Rojas
Keyword(s):  
Three Dimensional ◽  
Hydraulic Modeling ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
One Dimensional ◽  
Ansys Cfx ◽  
Combined Sewer ◽  
The One ◽  
Swmm Model

This study proposes a methodology for the calibration of combined sewer overflow (CSO), incorporating the results of the three-dimensional ANSYS CFX model in the SWMM one-dimensional model. The procedure consists of constructing calibration curves in ANSYS CFX that relate the input flow to the CSO with the overflow, to then incorporate them into the SWMM model. The results obtained show that the behavior of the flow over the crest of the overflow weir varies in space and time. Therefore, the flow of entry to the CSO and the flow of excesses maintain a non-linear relationship, contrary to the results obtained in the one-dimensional model. However, the uncertainty associated with the idealization of flow methodologies in one dimension is reduced under the SWMM model with kinematic wave conditions and simulating CSO from curves obtained in ANSYS CFX. The result obtained facilitates the calibration of combined sewer networks for permanent or non-permanent flow conditions, by means of the construction of curves in a three-dimensional model, especially when the information collected in situ is limited.

On the Recovery of 3D Spatial Statistics of Particles from 1D Measurements: Implications for Airborne Instruments

2014 ◽  
Vol 31 (10) ◽  
pp. 2078-2087 ◽  
Author(s):  
Michael L. Larsen ◽  
Clarissa A. Briner ◽  
Philip Boehner
Keyword(s):  
Point Processes ◽  
Pair Correlation ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Dimensional System ◽  
Cloud Droplets ◽  
Sampling Variability ◽  
One Dimensional ◽  
Natural Sampling ◽  
The One

Abstract The spatial positions of individual aerosol particles, cloud droplets, or raindrops can be modeled as a point processes in three dimensions. Characterization of three-dimensional point processes often involves the calculation or estimation of the radial distribution function (RDF) and/or the pair-correlation function (PCF) for the system. Sampling these three-dimensional systems is often impractical, however, and, consequently, these three-dimensional systems are directly measured by probing the system along a one-dimensional transect through the volume (e.g., an aircraft-mounted cloud probe measuring a thin horizontal “skewer” through a cloud). The measured RDF and PCF of these one-dimensional transects are related to (but not, in general, equal to) the RDF/PCF of the intrinsic three-dimensional systems from which the sample was taken. Previous work examined the formal mathematical relationship between the statistics of the intrinsic three-dimensional system and the one-dimensional transect; this study extends the previous work within the context of realistic sampling variability. Natural sampling variability is found to constrain substantially the usefulness of applying previous theoretical relationships. Implications for future sampling strategies are discussed.

Syntheses, Crystal Structures and Luminescent Properties of Two Isostructural Fluorinated Metal–organic Frameworks Based on Mixed 2,3,5,6-tetrafluoro-1,4-bis(imidazole-1-yl-methyl)Benzene and Oxalate Ligands

2016 ◽  
Vol 40 (12) ◽  
pp. 763-766
Author(s):  
Sheng-Chun Chen ◽  
Feng Tian ◽  
Ming-Yang He ◽  
Qun Chen
Keyword(s):  
Fluorescence Spectra ◽  
Metal Organic Frameworks ◽  
Luminescent Properties ◽  
Hydrothermal Conditions ◽  
One Dimensional ◽  
Metal Organic ◽  
Solid State Fluorescence ◽  
The One ◽  
Methyl Benzene

Two isostructural fluorinated metal-organic frameworks [M(Fbix)(ox)]n (where M = Zn or Mn, Fbix = 2,3,5,6-tetrafluoro-1,4-bis(imidazole-1-yl-methyl)benzene, ox = oxalate) have been synthesised from Fbix and oxamide under hydrothermal conditions, where oxalate is generated by the in situ hydrolysation of oxamide. The complexes are isostructural and display similar two-dimensional undulating sql nets formed by pillaring the one-dimensional [M(ox)]n chains through Fbix linkers. Their solid-state fluorescence spectra indicate a ligand-based emission for both complexes.

On a Class of Models for the Yielding Behavior of Continuous and Composite Systems

1967 ◽  
Vol 34 (3) ◽  
pp. 612-617 ◽  
Author(s):  
W. D. Iwan
Keyword(s):  
Steady State ◽  
Bauschinger Effect ◽  
Three Dimensions ◽  
Cyclic Behavior ◽  
One Dimensional ◽  
Composite Systems ◽  
Yielding Behavior ◽  
Nonsteady State ◽  
The One ◽  
Incremental Theory Of Plasticity

A class of one-dimensional models for the yielding behavior of materials and structures is presented. This class of models leads to stress-strain relations which exhibit a Bauschinger effect of the Massing type, and both the steady-state and nonsteady-state cyclic behavior are completely specified if the initial monotonic loading behavior is known. The concepts of the one-dimensional class of models are extended to three-dimensions and lead to a subsequent generalization of the customary concepts of the incremental theory of plasticity.

Diffraction of Electrons by Two and Three Mutually Orthogonal Standing Light Waves

1975 ◽  
Vol 53 (2) ◽  
pp. 157-164 ◽  
Author(s):  
F. Ehlotzky
Keyword(s):  
Electron Scattering ◽  
Light Wave ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Dimensional Problem ◽  
One Dimensional ◽  
Standing Light Wave ◽  
Light Waves ◽  
The One ◽  
Rectangular Lattices

The one-dimensional problem of electron scattering by a standing light wave, known as the Kapitza–Dirac effect, is shown to be easily extendable to two and three dimensions, thus showing all characteristics of diffraction of electrons by simple two- and three-dimensional rectangular lattices.

scholarly journals HIGH-FIELD LIMIT OF THE VLASOV–POISSON–FOKKER–PLANCK SYSTEM: A COMPARISON OF DIFFERENT PERTURBATION METHODS

2001 ◽  
Vol 11 (08) ◽  
pp. 1457-1468 ◽  
Author(s):  
LUIS L. BONILLA ◽  
JUAN S. SOLER
Keyword(s):  
High Field ◽  
Three Dimensions ◽  
Field Limit ◽  
One Dimensional ◽  
System A ◽  
Reduced Equations ◽  
Hilbert Expansion ◽  
The One ◽  
Different Order ◽  
Fokker Planck

A reduced drift-diffusion (Smoluchowski–Poisson) equation is found for the electric charge in the high-field limit of the Vlasov–Poisson–Fokker–Planck system, both in one and three dimensions. The corresponding electric field satisfies a Burgers equation. Three methods are compared in the one-dimensional case: Hilbert expansion, Chapman–Enskog procedure and closure of the hierarchy of equations for the moments of the probability density. Of these methods, only the Chapman–Enskog method is able to systematically yield reduced equations containing terms of different order.

INSTANTONS AND SPHALERONS IN SKYRMED WEINBERG–SALAM MODELS AND GRASSMANNIAN MODELS

2000 ◽  
Vol 15 (02) ◽  
pp. 251-264
Author(s):  
F. BRAU ◽  
V. BRIHAYE ◽  
D. H. TCHRAKIAN
Keyword(s):  
Higgs Doublet ◽  
Three Dimensions ◽  
Dimensional System ◽  
One Dimensional ◽  
Yang Mills ◽  
Pure Gauge ◽  
Static Solutions ◽  
The One ◽  
Matter Fields

Several Lagrangians describing the SU(2) Yang–Mills (YM) field interacting with matter are considered, which support both instantons (in four Euclidean dimensions) and sphaleron (in three dimensions, static) solutions. The matter fields are the complex Higgs doublet for the Weinberg–Salam (WS) model, and a (2 × 4) Grassmannian model. These Lagrangians feature Skyrme-like extensions to enable the existence of the instantons, which decay as pure gauge at infinity. For two of these models, we have numerically integrated the one-dimensional system arising from the imposition of radial ansatz.

The three-dimensional hydrogen-bonded structures in the ammonium and sodium salt hydrates of 4-aminophenylarsonic acid

2014 ◽  
Vol 70 (8) ◽  
pp. 738-741 ◽  
Author(s):  
Graham Smith ◽  
Urs D. Wermuth
Keyword(s):  
Hydrogen Bonding ◽  
Sodium Salt ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Dimensional Structure ◽  
Water Molecules ◽  
One Dimensional ◽  
Arsanilic Acid ◽  
Hydrogen Bonding Interactions ◽  
The One

The structures of two hydrated salts of 4-aminophenylarsonic acid (p-arsanilic acid), namely ammonium 4-aminophenylarsonate monohydrate, NH4+·C6H7AsNO3−·H2O, (I), and the one-dimensional coordination polymercatena-poly[[(4-aminophenylarsonato-κO)diaquasodium]-μ-aqua], [Na(C6H7AsNO3)(H2O)3]n, (II), have been determined. In the structure of the ammonium salt, (I), the ammonium cations, arsonate anions and water molecules interact through inter-species N—H...O and arsonate and water O—H...O hydrogen bonds, giving the common two-dimensional layers lying parallel to (010). These layers are extended into three dimensions through bridging hydrogen-bonding interactions involving thepara-amine group acting both as a donor and an acceptor. In the structure of the sodium salt, (II), the Na+cation is coordinated by five O-atom donors, one from a single monodentate arsonate ligand, two from monodentate water molecules and two from bridging water molecules, giving a very distorted square-pyramidal coordination environment. The water bridges generate one-dimensional chains extending alongcand extensive interchain O—H...O and N—H...O hydrogen-bonding interactions link these chains, giving an overall three-dimensional structure. The two structures reported here are the first reported examples of salts ofp-arsanilic acid.

scholarly journals THE VISCOUS MODEL OF QUANTUM HYDRODYNAMICS IN SEVERAL DIMENSIONS

2007 ◽  
Vol 17 (07) ◽  
pp. 1065-1093 ◽  
Author(s):  
LI CHEN ◽  
MICHAEL DREHER
Keyword(s):  
Periodic Boundary Conditions ◽  
Higher Dimensions ◽  
Three Dimensions ◽  
Quantum Hydrodynamics ◽  
Existence Of A Solution ◽  
Thermal Equilibrium State ◽  
One Dimensional ◽  
Entropy Dissipation ◽  
The One ◽  
Time Existence

We investigate the viscous model of quantum hydrodynamics in one and higher space dimensions. Exploiting the entropy dissipation method, we prove the exponential decay to the thermal equilibrium state in one, two, and three dimensions, provided that the domain is a box. Further, we show the local in time existence of a solution in the one-dimensional case; and in the case of higher dimensions under the assumption of periodic boundary conditions. Finally, we prove the global existence in a one-dimensional setting under additional assumptions.

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