scholarly journals Stochastic Analysis of a Nonlocal Fractional Viscoelastic Bar Forced by Gaussian White Noise

2017 ◽  
Vol 3 (3) ◽  
Author(s):  
G. Alotta ◽  
G. Failla ◽  
F. P. Pinnola
Keyword(s):  
Finite Element ◽  
White Noise ◽  
Long Range ◽  
Gaussian White Noise ◽  
Local Stress ◽  
Transverse Motion ◽  
The Finite Element Method ◽  
Range Interaction ◽  
Long Range Interactions ◽  
Displacement Based

Recently, a displacement-based nonlocal bar model has been developed. The model is based on the assumption that nonlocal forces can be modeled as viscoelastic (VE) long-range interactions mutually exerted by nonadjacent bar segments due to their relative motion; the classical local stress resultants are also present in the model. A finite element (FE) formulation with closed-form expressions of the elastic and viscoelastic matrices has also been obtained. Specifically, Caputo's fractional derivative has been used in order to model viscoelastic long-range interaction. The static and quasi-static response has been already investigated. This work investigates the stochastic response of the nonlocal fractional viscoelastic bar introduced in previous papers, discretized with the finite element method (FEM), forced by a Gaussian white noise. Since the bar is forced by a Gaussian white noise, dynamical effects cannot be neglected. The system of coupled fractional differential equations ruling the bar motion can be decoupled only by means of the fractional order state variable expansion. It is shown that following this approach Monte Carlo simulation can be performed very efficiently. For simplicity, here the work is limited to the axial response, but can be easily extended to transverse motion.

Statistical theory of adsorption with long-range interaction

1938 ◽  
Vol 34 (2) ◽  
pp. 238-252 ◽  
Author(s):  
J. S. Wang
Keyword(s):  
Statistical Theory ◽  
Long Range ◽  
Unit Area ◽  
Continuous Distribution ◽  
Lattice Points ◽  
Circular Region ◽  
Range Interaction ◽  
Dipole Interactions ◽  
Long Range Interactions ◽  
Long Range Interaction

The statistical theory of long-range interactions between adsorbed particles on a plane lattice is worked out approximately, by treating in detail the distribution of adsorbed particles among a few sites inside and on the boundary of a circular region, and regarding the distribution outside the circle as uniform and continuous with a density Kθ per unit area, where K is the number of lattice points per unit area and θ is the fraction of surface covered by adsorbed particles. The continuous distribution begins at a distance ρ from the centre of the circle, ρ being determined by the condition that the probability of occupation of a first shell site is equal to the probability θ of occupation of the central site. Using this method, general formulae for the adsorption isotherm and the heat of adsorption are obtained. Numerical applications for dipole interactions and for quadratic and hexagonal lattices are worked out in detail and the case in which the dipole moment varies with θ is discussed.

LONG-RANGE INTERACTIONS IN THE HELICOIDAL DNA DYNAMICS

2013 ◽  
Vol 27 (24) ◽  
pp. 1350143 ◽  
Author(s):  
MIRABEAU SAHA ◽  
TIMOLEON C. KOFANÉ
Keyword(s):  
Rna Polymerase ◽  
Long Range ◽  
Power Law ◽  
Dna Dynamics ◽  
Extended Version ◽  
Range Interaction ◽  
Dna Molecule ◽  
Long Range Interactions ◽  
Long Range Interaction

In this paper, the comparison between power-law long-range interaction and Kac–Baker long-range interaction in the DNA molecule is investigated. This is done by employing an extended version of spin-like model of the DNA molecule with long-range interaction between intra-strand nucleotides and helicoidal coupling between inter-strand nucleotides when an RNA-polymerase binds to the DNA at biological temperature. Results show that LRIs have an undeniable effect on the DNA dynamics and that one is free to use either PLLRI or KBLRI to study DNA behaviors.

scholarly journals Engineering long-range interactions between ultracold atoms with light

2022 ◽  
Author(s):  
Ting XIE ◽  
Andrea Orbán ◽  
Xiaodong Xing ◽  
Eliane Luc-Koenig ◽  
Romain Vexiau ◽  
...  
Keyword(s):  
Long Range ◽  
Ultracold Atoms ◽  
Quantum Gases ◽  
Atomic Gases ◽  
Complete Suppression ◽  
Atomic Collisions ◽  
Range Interaction ◽  
Long Range Interactions ◽  
To Come ◽  
A Minor

Abstract Ultracold temperatures in dilute quantum gases opened the way to an exquisite control of matter at the quantum level. Here we focus on the control of ultracold atomic collisions using a laser to engineer their interactions at large interatomic distances. We show that the entrance channel of two colliding ultracold atoms can be coupled to a repulsive collisional channel by the laser light so that the overall interaction between the two atoms becomes repulsive: this prevents them to come close together and to undergo inelastic processes, thus protecting the atomic gases from unwanted losses. We illustrate such an optical shielding mechanism with 39K and 133Cs atoms colliding at ultracold temperature (<1 microkelvin). The process is described in the framework of the dressed-state picture and we then solve the resulting stationary coupled Schrödinger equations. The role of spontaneous emission and photoinduced inelastic scattering is also investigated as possible limitations of the shielding efficiency. We predict an almost complete suppression of inelastic collisions over a broad range of Rabi frequencies and detunings from the 39K D2 line of the optical shielding laser, both within the [0, 200 MHz] interval. We found that the polarization of the shielding laser has a minor influence on this efficiency. This proposal could easily be formulated for other bialkali-metal pairs as their long-range interaction are all very similar to each other.

Single-mutation-induced stability loss in protein lysozyme

2007 ◽  
Vol 35 (6) ◽  
pp. 1551-1557 ◽  
Author(s):  
L. Ye ◽  
Z. Wu ◽  
M. Eleftheriou ◽  
R. Zhou
Keyword(s):  
Molecular Mechanism ◽  
Long Range ◽  
Large Scale ◽  
Stability Loss ◽  
Single Mutation ◽  
Wild Type ◽  
Range Interaction ◽  
Local Cluster ◽  
Long Range Interactions ◽  
Arginine Residues

Recent NMR experiments have revealed that a single residue mutation W62G on protein hen's-egg white lysozyme can cause a dramatic loss of long-range interactions and protein stability; however, the molecular mechanism for this surprising phenomenon is not completely clear. In this mini-review, we have summarized some of our recent work on the molecular mechanism with large-scale molecular modelling, and also utilized a new wavelet method to analyse the local structural clusters present in both the wild-type and mutant folding trajectories. These extensive MD (Molecular Dynamics) simulations (10+ μs) were performed in 8 M urea, mimicking the experimental condition. Detailed analyses revealed that the Trp62 residue is the key to a co-operative long-range interaction within the wild-type protein: it acts as a bridge between neighbouring basic residues, mainly arginine residues, through π-type hydrogen bonds or π-cation interactions to form an Arg-Trp-Arg ‘sandwich-like’ local structure. The local cluster near Trp62 further extends its interaction to other clusters, such as the one near Trp111, through Arg112, which is involved in such an Arg-Trp-Arg bridging structure, thus achieving the long-range interactions for the wild-type. On the other hand, the mutant does not have this bridging effect and forms much less local clusters or contacts, and therefore results in a much less stable structure. Overall, these findings not only support the general conclusions of the experiment, but also provide a detailed but somewhat different molecular picture of the disruption of the long-range interactions.

Finite Element Analysis for Demolding Process in Thermal Imprint Lithography

2007 ◽  
Author(s):  
Zhichao Song ◽  
Jaejong Lee ◽  
Sunggook Park
Keyword(s):  
Finite Element ◽  
Contact Region ◽  
Substrate Surface ◽  
Mold Insert ◽  
Local Stress ◽  
Imprint Lithography ◽  
Structural Failure ◽  
The Finite Element Method ◽  
Element Analysis ◽  
The Ideal

In thermal imprint lithography, most of the imprint failures occur during demolding, a process to separate the mold insert from the substrate after conformal molding. The success of demolding is determined by the stress generated in the resist with respect to the yield stress of the resist. In this paper we simulated the demolding process in thermal imprint lithography using the finite element method to study the stress distribution and deformation in poly(methyl methacrylate) (PMMA) resist during demolding. During demolding, the stress concentrates both at the transition corner zone between the residual layer and the replicated pattern, and close to the contact region with the moving stamp. As demolding proceeds, the highest local stress for both locations shows two maximums, indicating that a structural failure may occur not only when demolding starts, but also immediately before demolding ends. The structural failure at the second maximum becomes dominant as the angular offset from the ideal normal demolding to the substrate surface increases or for the structures located far away from the symmetric centerline. In addition, we will discuss the influence of other process and geometry parameters, including demolding rate and stamp aspect ratio.

scholarly journals A Hepatitis C Virus cis-Acting Replication Element Forms a Long-Range RNA-RNA Interaction with Upstream RNA Sequences in NS5B

2008 ◽  
Vol 82 (18) ◽  
pp. 9008-9022 ◽  
Author(s):  
Sinéad Diviney ◽  
Andrew Tuplin ◽  
Madeleine Struthers ◽  
Victoria Armstrong ◽  
Richard M. Elliott ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Long Range ◽  
Upstream Region ◽  
Fundamental Aspect ◽  
Genome Replication ◽  
Range Interaction ◽  
Stem Loop ◽  
Long Range Interactions ◽  
Rna Interaction

ABSTRACT The genome of hepatitis C virus (HCV) contains cis-acting replication elements (CREs) comprised of RNA stem-loop structures located in both the 5′ and 3′ noncoding regions (5′ and 3′ NCRs) and in the NS5B coding sequence. Through the application of several algorithmically independent bioinformatic methods to detect phylogenetically conserved, thermodynamically favored RNA secondary structures, we demonstrate a long-range interaction between sequences in the previously described CRE (5BSL3.2, now SL9266) with a previously predicted unpaired sequence located 3′ to SL9033, approximately 200 nucleotides upstream. Extensive reverse genetic analysis both supports this prediction and demonstrates a functional requirement in genome replication. By mutagenesis of the Con-1 replicon, we show that disruption of this alternative pairing inhibited replication, a phenotype that could be restored to wild-type levels through the introduction of compensating mutations in the upstream region. Substitution of the CRE with the analogous region of different genotypes of HCV produced replicons with phenotypes consistent with the hypothesis that both local and long-range interactions are critical for a fundamental aspect of genome replication. This report further extends the known interactions of the SL9266 CRE, which has also been shown to form a “kissing loop” interaction with the 3′ NCR (P. Friebe, J. Boudet, J. P. Simorre, and R. Bartenschlager, J. Virol. 79:380-392, 2005), and suggests that cooperative long-range binding with both 5′ and 3′ sequences stabilizes the CRE at the core of a complex pseudoknot. Alternatively, if the long-range interactions were mutually exclusive, the SL9266 CRE may function as a molecular switch controlling a critical aspect of HCV genome replication.

scholarly journals Resting state MEG oscillations show long-range temporal correlations of phase synchrony that break down during finger-tapping

2015 ◽  
Author(s):  
Maria Botcharova ◽  
Luc Berthouze ◽  
Matthew J Brookes ◽  
Gareth R Barnes ◽  
Simon F Farmer
Keyword(s):  
White Noise ◽  
Long Range ◽  
Phase Difference ◽  
Resting State ◽  
Temporal Structure ◽  
Gaussian White Noise ◽  
Kuramoto Model ◽  
Finger Tapping ◽  
Temporal Correlations ◽  
Left And Right

The capacity of the human brain to interpret and respond to multiple temporal scales in its surroundings suggests that its internal interactions must also be able to operate over a broad temporal range. In this paper, we utilise a recently introduced method for characterising the rate of change of the phase difference between MEG signals and use it to study the temporal structure of the phase interactions between MEG recordings from the left and right motor cortices during rest and during a finger-tapping task. We use the Hilbert transform to estimate moment-to-moment fluctuations of the phase difference between signals. After confirming the presence of scale-invariance we estimate the Hurst exponent using detrended fluctuation analysis (DFA). An exponent of >0.5 is indicative of long-range temporal correlations (LRTCs) in the signal. We find that LRTCs are present in the α/μ and β frequency bands of resting state MEG data. We demonstrate that finger movement disrupts LRTCs correlations, producing a phase relationship with a structure similar to that of Gaussian white noise. The results are validated by applying the same analysis to data with Gaussian white noise phase difference, recordings from an empty scanner and phase-shuffled time series. We interpret the findings through comparison of the results with those we obtained from an earlier study during which we adopted this method to characterise phase relationships within a Kuramoto model of oscillators in its sub-critical, critical and super-critical synchronisation states. We find that the resting state MEG from left and right motor cortices shows moment-to-moment fluctuations of phase difference with a similar temporal structure to that of a system of Kuramoto oscillators just prior to its critical level of coupling, and that finger tapping moves the system away from this pre-critical state towards a more random state.

q-Gaussian approximants mimic non-extensive statistical-mechanical expectation for many-body probabilistic model with long-range correlations

Open Physics ◽  
2009 ◽  
Vol 7 (3) ◽  
Author(s):  
William Thistleton ◽  
John Marsh ◽  
Kenric Nelson ◽  
Constantino Tsallis
Keyword(s):  
Long Range ◽  
Gaussian Distribution ◽  
Random Variables ◽  
Present System ◽  
Many Body ◽  
Scale Invariant ◽  
Range Interaction ◽  
Multivariate Gaussian Distribution ◽  
Long Range Correlations ◽  
Long Range Interactions

AbstractWe study a strictly scale-invariant probabilistic N-body model with symmetric, uniform, identically distributed random variables. Correlations are induced through a transformation of a multivariate Gaussian distribution with covariance matrix decaying out from the unit diagonal, as ρ/r α for r =1, 2, ..., N-1, where r indicates displacement from the diagonal and where 0 ⩽ ρ ⩽ 1 and α ⩾ 0. We show numerically that the sum of the N dependent random variables is well modeled by a compact support q-Gaussian distribution. In the particular case of α = 0 we obtain q = (1-5/3 ρ) / (1- ρ), a result validated analytically in a recent paper by Hilhorst and Schehr. Our present results with these q-Gaussian approximants precisely mimic the behavior expected in the frame of non-extensive statistical mechanics. The fact that the N → ∞ limiting distributions are not exactly, but only approximately, q-Gaussians suggests that the present system is not exactly, but only approximately, q-independent in the sense of the q-generalized central limit theorem of Umarov, Steinberg and Tsallis. Short range interaction (α > 1) and long range interactions (α < 1) are discussed. Fitted parameters are obtained via a Method of Moments approach. Simple mechanisms which lead to the production of q-Gaussians, such as mixing, are discussed.

scholarly journals Improving Chromatin-Interaction Prediction Using Single-Cell Open-Chromatin Profiles and Making Insight Into the Cis-Regulatory Landscape of the Human Brain

2021 ◽  
Vol 12 ◽  
Author(s):  
Neetesh Pandey ◽  
Omkar Chandra ◽  
Shreya Mishra ◽  
Vibhor Kumar
Keyword(s):  
Human Brain ◽  
Single Cell ◽  
Long Range ◽  
Target Genes ◽  
Interaction Analysis ◽  
Chromatin Interaction ◽  
Open Chromatin ◽  
Cell Type ◽  
Range Interaction ◽  
Long Range Interactions

Single-cell open-chromatin profiles have the potential to reveal the pattern of chromatin-interaction in a cell type. However, currently available cis-regulatory network prediction methods using single-cell open-chromatin profiles focus more on local chromatin interactions despite the fact that long-range interactions among genomic sites play a significant role in gene regulation. Here, we propose a method that predicts both short and long-range interactions among genomic sites using single-cell open chromatin profiles. Our method, termed as single-cell epigenome based chromatin-interaction analysis (scEChIA) exploits signal imputation and refined L1 regularization. For a few single-cell open-chromatin profiles, scEChIA outperformed other tools even in terms of accuracy of prediction. Using scEChIA, we predicted almost 0.7 million interactions among genomic sites across seven cell types in the human brain. Further analysis revealed cell type for connection between genes and expression quantitative trait locus (eQTL) in the human brain and making insight about target genes of human-accelerated-elements and disease-associated mutations. Our analysis enabled by scEChIA also hints about the possible action of a few transcription factors (TFs), especially through long-range interaction in brain endothelial cells.

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