Folding Model Research Articles

Fiber-Like Organization as a Basic Principle for Euchromatin Higher-Order Structure.

A detailed understanding of the principles of the structural organization of genetic material is of great importance for elucidating the mechanisms of differential regulation of genes in development. Modern ideas about the spatial organization of the genome are based on a microscopic analysis of chromatin structure and molecular data on DNA–DNA contact analysis using Chromatin conformation capture (3C) technology, ranging from the “polymer melt” model to a hierarchical folding concept. Heterogeneity of chromatin structure depending on its functional state and cell cycle progression brings another layer of complexity to the interpretation of structural data and requires selective labeling of various transcriptional states under nondestructive conditions. Here, we use a modified approach for replication timing-based metabolic labeling of transcriptionally active chromatin for ultrastructural analysis. The method allows pre-embedding labeling of optimally structurally preserved chromatin, thus making it compatible with various 3D-TEM techniques including electron tomography. By using variable pulse duration, we demonstrate that euchromatic genomic regions adopt a fiber-like higher-order structure of about 200 nm in diameter (chromonema), thus providing support for a hierarchical folding model of chromatin organization as well as the idea of transcription and replication occurring on a highly structured chromatin template.

A Maximum Caliber analysis of the Foldon Hypothesis

Different models of protein folding favor different mechanisms. Some models rely on a defined pathway, while other models rely on a more heterogeneous set of pathways. The Foldon Hypothesis is based on the concept of a defined pathway. According to the Foldon Hypothesis, protein folding is characterized by the stepwise assembly of small, cooperative units called foldons. The Maximum Caliber (Max Cal) method provides an opportunity to test this model. The Max Cal method gives the probabilities for dynamical trajectories, in much the same way that the maximum entropy principle gives the probabilities for equilibrium states. In this study, the Max Cal method was applied to folding data for the protein cytochrome c (cyt c; Hu W, Kan ZY, Mayne L, Englander SW. Proc Natl Acad Sci U S A. 2016;113:3809-3814). The overall picture to emerge from this analysis is that the data do not require a dominant, defined pathway. The folding of cytochrome c is likely a heterogeneous process that includes multiple pathways.

Evolving cellular automata schemes for protein folding modeling using the Rosetta atomic representation

Protein folding is the dynamic process by which a protein folds into its final native structure. This is different to the traditional problem of the prediction of the final protein structure, since it requires a modeling of how protein components interact over time to obtain the final folded structure. In this study we test whether a model of the folding process can be obtained exclusively through machine learning. To this end, protein folding is considered as an emergent process and the cellular automata tool is used to model the folding process. A neural cellular automaton is defined, using a connectionist model that acts as a cellular automaton through the protein chain to define the dynamic folding. Differential evolution is used to automatically obtain the optimized neural cellular automata that provide protein folding. We tested the methods with the Rosetta coarse-grained atomic model of protein representation, using different proteins to analyze the modeling of folding and the structure refinement that the modeling can provide, showing the potential advantages that such methods offer, but also difficulties that arise.

Neutron skin in 48Ca determined from p+48Ca and 48Ca+12C scattering

Background:In our previous paper, we determined rskin208(exp)=0.278±0.035 fm from measured reaction cross sections σR for p+208Pb scattering, using the Kyushu (chiral) g-matrix folding model with the densities calculated with the Gogny-D1S Hartree–Fock–Bogoliubov (D1S-GHFB) with the angular momentum projection (AMP). The value agrees with that of PREX2. Reaction cross sections σR are available for p+48Ca scattering, whereas interaction cross sections σI(≈σR) are available for 48Ca + 12C scattering. As for 48Ca, the high-resolution E1 polarizability experiment (E1pE) yields rskin48(E1pE)=0.14∼0.20fm. Purpose:We determine rskin48(exp) from the data on σR for p+48Ca scattering and from the data on σI for 48Ca+12C scattering. Methods:We use the Kyushu g-matrix folding model with the densities calculated with the D1M-GHFB+AMP densities. The D1M-GHFB+AMP proton and neutron densities are scaled so as to reproduce the data under the condition that the radius rp of the scaled proton density equals the data rp(exp) determined from the electron scattering. We deduce skin values rskin=rn(exp)−rp(exp) from the resulting rn(exp) and the rp(exp) determined from electron scattering. The same procedure is taken for D1S-GHFB+AMP. Results:We regard rskin48(E1pE) as a reference skin value. Using the reference skin value and taking D1M-GHFB+AMP, we determine rskin48(exp)=0.158±0.025 fm for p+48Ca scattering and 0.160±0.058 fm for 48Ca +12C scattering. Conclusion:We take the weighted mean and its error for the two skin values. The result is rskin48(exp)=0.158±(0.023)exp±(0.012)thfm.

Folding-model approach to reaction cross section of [formula omitted]He+12C scattering at 790 MeV

Tanihata et al. (1988) determined matter radii rm(σI) for 4,6,8He from interaction cross sections σI of 4,6,8He+12C scattering at 790 MeV per nucleon, using the optical limit of the Glauber model. Lu et al. (2013) determined proton radii rp(AIS) for 4,6,8He with the atomic isotope shifts (AIS). We investigate whether the Love-Franey t-matrix folding model is good for 4,6,8He+12C scattering at 790 MeV per nucleon.

Constraining the α-nucleus potential for α-decay calculation with nuclear rainbow scattering

Introduction: The emission of a particles is a powerful probe for the α-cluster structure of heavy nuclei. The α-nucleus potential is a crucial ingredient in the a-decay calculation within the preformed cluster model. One of the most reliable ways to construct this potential is the double folding model, where an effective nucleon-nucleon interaction is folded with the nuclear densities. In the folding model calculation, there are many ambiguities in the choice of the nuclear densities of the daughter nucleus for α-decay. We propose to directly constrain the α-nucleus potential for α- decay and choose the daughter nuclear density using the nuclear rainbow scattering phenomenon. Methods: The refractive rainbow pattern in the elastic scattering cross section within the optical model can probe deep into the interior region of the α-nucleus potential. We apply this method to investigate the reliability of the nuclear potential used in the α-decay of the 212Po nucleus leading to the 208Pb daughter nucleus by examining the elastic a scattering on 208Pb. In such an approach, we perform the double-folding calculation to construct the α-nucleus potential using several common parametrizations of the daughter nuclear densities. These parametrizations include the mean-field Hartree-Fock-Bogoliubov calculations with the BSk14 and D1S interactions, the independent particle model, and the 2-parameter Fermi distributions. The obtained nuclear potentials are applied to the optical model to calculate the elastic α-208Pb scattering cross sections that are compared with the experimental data. These nuclear potentials are further used in the preformed cluster model to study thea-decay half-life of 212Po. Results: The nuclear densities from the Hartree-Fock-Bogoliubov calculations are shown to provide the best description for both the nuclear rainbow scattering anda-decay half-life. The results indicate a strong correspondence between the capabilities of the nuclear potential to reproduce the cross section ofa scattering and the α-decay half-life. The extracteda preformation factors from the semiclassical preformed cluster model with folding potentials are in good agreement with those from other studies. Conclusion: The nuclear rainbow scattering phenomenon can be used to provide reliable a-nucleus potential for α-decay studies within the preformed cluster model. The nuclear densities from the mean-field Hartree-Fock-Bogoliubov method with the BSk14 and D1S interactions are the appropriate choices for the DFM calculation used in the α-decay study.

Multi-scale phase separation by explosive percolation with single-chromatin loop resolution

The 2 m-long human DNA is tightly intertwined into the cell nucleus of the size of 10 μm. The DNA packing is explained by folding of chromatin fiber. This folding leads to the formation of such hierarchical structures as: chromosomal territories, compartments; densely-packed genomic regions known as Topologically Associating Domains (TADs), or Chromatin Contact Domains (CCDs), and loops. We propose models of dynamical human genome folding into hierarchical components in human lymphoblastoid, stem cell, and fibroblast cell lines. Our models are based on explosive percolation theory. The chromosomes are modeled as graphs where CTCF chromatin loops are represented as edges. The folding trajectory is simulated by gradually introducing loops to the graph following various edge addition strategies that are based on topological network properties, chromatin loop frequencies, compartmentalization, or epigenomic features. Finally, we propose the genome folding model - a biophysical pseudo-time process guided by a single scalar order parameter. The parameter is calculated by Linear Discriminant Analysis of chromatin features. We also include dynamics of loop formation by using Loop Extrusion Model (LEM) while adding them to the system. The chromatin phase separation, where fiber folds in 3D space into topological domains and compartments, is observed when the critical number of contacts is reached. We also observe that at least 80% of the loops are needed for chromatin fiber to condense in 3D space, and this is constant through various cell lines. Overall, our in-silico model integrates the high-throughput 3D genome interaction experimental data with the novel theoretical concept of phase separation, which allows us to model event-based time dynamics of chromatin loop formation and folding trajectories.

Triangular body-cover model of the vocal folds with coordinated activation of the five intrinsic laryngeal muscles.

Poor laryngeal muscle coordination that results in abnormal glottal posturing is believed to be a primary etiologic factor in common voice disorders such as non-phonotraumatic vocal hyperfunction. Abnormal activity of antagonistic laryngeal muscles is hypothesized to play a key role in the alteration of normal vocal fold biomechanics that results in the dysphonia associated with such disorders. Current low-order models of the vocal folds are unsatisfactory to test this hypothesis since they do not capture the co-contraction of antagonist laryngeal muscle pairs. To address this limitation, a self-sustained triangular body-cover model with full intrinsic muscle control is introduced. The proposed scheme shows good agreement with prior studies using finite element models, excised larynges, and clinical studies in sustained and time-varying vocal gestures. Simulations of vocal fold posturing obtained with distinct antagonistic muscle activation yield clear differences in kinematic, aerodynamic, and acoustic measures. The proposed tool is deemed sufficiently accurate and flexible for future comprehensive investigations of non-phonotraumatic vocal hyperfunction and other laryngeal motor control disorders.

Experimental model for controlled endoscopic subepithelial vocal fold injury in rats.

ABSTRACTPurpose:To present a detailed, reproducible, cost-efficient surgical model for controlled subepithelial endoscopic vocal fold injury in the rat model.Methods:Six male Sprague Dawley rats were enrolled in the experiment. The left vocal folds were used to carry out the injury model, and the right vocal fold served as control. After deep sedation, the rats were placed on a custom operating platform. The vocal fold injury by subepithelial stripping was carried out using custom-made microsurgical instruments under endoscopic guidance. Data were analyzed for procedural time and post-procedural pain. Microcomputed tomography (micro-CT) scan and histologic images were obtained to assess the length, area, and depth of injury to the vocal fold.Results:The mean procedural time was 112 s. The mean control vocal fold length was 0.96 ± 0.04 mm. The mean vocal fold injury length was 0.53 ± 0.04 mm. The mean vocal fold surface was 0.18 ± 0.01 mm2 with a mean lesion area of 0.05 ± 0.00 mm2. Mean vocal fold injury depth was 375.4 ± 42.8 μm. The lesion length to vocal fold length ratio was 0.55 ± 0.03, as well as lesion area to vocal fold surface area was 0.29 ± 0.02.Conclusions:Our described experimental vocal fold injury model in rats is found to be fast, safe, cost-efficient, and reproducible with a rapid learning curve.

The α-decay half-lives of heavy nuclei via the double folding model with the use of relativistic NN interactions

In this study, the half-lives of [Formula: see text]-decay from some heavy nuclei in the range [Formula: see text] have been studied using the WKB semi-classical approximation. The nuclear interaction potential between the [Formula: see text]-particle and the daughter nuclei is obtained within the double folding model. The [Formula: see text] interactions employed are those derived from relativistic mean field (RMF) theory, called as R3Y [Formula: see text] interactions. Six different R3Y [Formula: see text] interactions are considered in the study to determine the most appropriate R3Y parametrization for heavy nuclei. Some of the R3Y interactions (such as R3Y-HS, R3Y-L1, R3Y-Z, R3Y-W) contain only linear [Formula: see text], [Formula: see text], and [Formula: see text] mesons, while the others (such as R3Y-NL2, R3Y-NLSH) contain nonlinear terms, in addition to the linear terms. All the R3Y [Formula: see text] interactions used are found to be efficient in describing the [Formula: see text]-decay half-lives data. However, R3Y [Formula: see text] interactions containing nonlinear terms are found to perform better than those containing only linear terms of the mesons.

BiInNet: Bilateral Inversion Network for Real-Time Velocity Analysis

Most previous studies focus on using complex deep neural networks to learn diverse features of massive synthetic data. In more realistic situations with a limited number of data pairs, complex networks not only have higher computational complexity, increasing training time and reducing inference speed, but also tend to over-fit a small amount of training data, thus having weak generalization capability. To address the aforementioned problem, we propose a lightweight architecture for real-time velocity inversion in realistic situations, the bilateral inversion network (BiInNet). BiInNet uses lightweight ResNet18, ShuffleNetV2, and modified MobileNetV2 as backbones, taking into account the inversion accuracy and inference speed. To reduce the redundant information in common shot gathers and focus on graphical property features which are strongly correlated with velocity, the intermediate results of velocity analysis, semblances, and interval velocity models are prepared as data pairs. Numerical experiments show that BiInNet can infer interval velocity models in real-time, with frames per second (FPS) up to 76.90 when ResNet18 is used as the backbone. Moreover, BiInNet achieves the best inversion accuracy on more realistic fold models, fault models, salt models, and noisy dataset (NFOMD) when adopting ShuffleNetV2 as the backbone, which illustrates that BiInNet can be applied to velocity inversion tasks of different geological structures and is robust to noise. Adopting transfer learning to fine-tune pretrained model, BiInNet is effectively applicable to velocity reversal models and field data, which further demonstrates the reliability of the proposed method and provides a practical velocity inversion scheme when the field data pairs are insufficient.

A New Modeling of Classical Folds in Computational Origami

This paper shows a cut along a crease on an origami sheet makes simple modeling of popular traditional basic folds such as a squash fold in computational origami. The cut operation can be applied to other classical folds and significantly simplify their modeling and subsequent implementation in the context of computational origami.

Active Remodeling of Chromatin and Implications for In Vivo Folding.

Building on the observation that chromatin compaction can be locally modulated by activity, we propose a model of in vivo chromatin as an active polymer and study its large scale conformations. In particular, we study an active mechanochemical model of chromosomal folding based on the interplay among polymer elasticity, confinement, topological constraints, and fluctuating active stresses arising from the ATP-dependent action of a variety of chromatin-associated protein machines and chromatin-remodeling proteins and their stochastic turnover. We find that activity drives the chromatin to a nonequilibrium steady state; the statistics of conformations in this nonequilibrium steady state are consistent with recent measurements on intrachromosomal contact probabilities and chromosomal compaction. The contact exponents at steady state show a systematic variation with changes in the nature of activity and the rates of turnover. The steady state configuration of the active chromatin in two dimensions resembles a space-filling Peano curve, which might have implications for the optimization of genome information storage.

Pauli blocking potential applied to heavy-ion fusion reactions * *Supported by the National Natural Science Foundation of China (12105080, 11822503, 11975091) and the Program for Innovative Research Team (in Science and Technology) in University of Henan Province (21IRTSTHN011), China

In this study, the Pauli blocking potential between two colliding nuclei in the density overlapping region is applied to describe the heavy nuclei fusion process. Inspired by the Pauli blocking effect in the -decay of heavy nuclei, the Pauli blocking potential of single nucleon from the surrounding matter is obtained. In fusion reactions with strong density overlap, the Pauli blocking potential between the projectile and target can be constructed using a single folding model. By considering this potential, the double folding model with a new parameter set is employed to analyze the fusion processes of 95 systems. A wider Coulomb barrier and shallower potential pocket are formed in the inner part of the potential between the two colliding nuclei, compared to that calculated using the Akyüz-Winther potential. The fusion hindrance phenomena at deep sub-barrier energies are described well for fusion systems O + Pb and Ni + Ni.

Post-Oligocene evolution of Indo-Burma wedge: Insights from deformation structures of Tripura Mizoram fold belt

The Tripura Mizoram fold belt (TMFB) belongs to the widest segment of the outer wedge of Indo-Burma Wedge (IBW). The structure of the outer wedge is characterized by a series of north-south trending anticlines-and-synclines of varying tightness, which progressively decreases towards the foreland direction. To explain their development, earlier workers proposed the model of fault-related folding, assuming that crustal shortening between India and Burma occurred dominantly by brittle deformation. However, our field investigations in TMFB reveal imprints of unequivocal ductile deformation, including interference of folds. Based on new structural map coupled with outcrop-scale structures, we recognize the existence of multi-ordered folds in the Neogene sequence of TMFB. However, the complexity of folding increases toward the hinterland part of wedge. We substantiate the spatial variations of penetrative ductile structures of TMFB with laboratory experiments under oblique convergence. Model results show consistency with the existence of along-strike variations of deformation intensity in the outer wedge of IBW, which gradually increases southward with narrowing the width of the wedge. Combining our field observations and laboratory experiments with earthquake focal depth distributions around TMFB, we propose that stratigraphic horizons of the entire outer wedge are mechanically weak to have deformed dominantly by brittle faulting.

A Comparison of Different Folding Models in Variations of the Map Folding Problem

In this paper, we compare the performance of three different folding models when they are applied to three different map folding settings. Precisely, the three folding models include the simple folding model, the simple folding–unfolding model, and the general folding model. The different map folding settings are discussed by comparing different folded states, i.e., different overlapping orders on the set of the squares of 1 × n maps, the squares of m × n maps, and the squares lying on the boundary of m × n maps. These folding models are abstracts of manual works and robotics. We clarify the relationship between their reachable final folded states under different settings and give proof of all the inclusion relationships between every two of these sets. In addition, there are nine distinct problems with the three folding models applied to three folding settings. We give the optimal linear time solutions to all the unsolved ones: the valid total overlapping order problems of 1 × n maps, m × n maps, as well as the valid boundary overlapping order problems of m × n maps with the three different folding models. Our work gives the conclusion of the research field where the folding models and the overlapping orders of map folding are concerned.

Synchronized and Desynchronized Dynamics Observed from Physical Models of the Vocal and Ventricular Folds

The ventricular folds, located superiorly to the vocal folds, do not usually vibrate during normal phonations. It has been shown, however, that they do vibrate together with the vocal folds under special circumstances such as voice pathology and singing voice. Towards understanding the effect of the ventricular fold oscillations on the vocal fold oscillations, the present study developed a synthetic model that takes into account anatomical features of the human ventricular folds. The synthetic model is made of flexible silicone compounds with material properties comparable to those of human ventricular fold tissues. In our experiment, an air-flow was injected into the vocal and ventricular fold models. As the distance between the left and right ventricular folds was reduced, the ventricular folds started to co-vibrate with the vocal folds. Depending upon the distance, various oscillation patterns of the vocal-ventricular folds were observed, e.g., synchronized dynamics with 1:1 or 1:2 frequency ratio and desynchronized chaotic dynamics. The observed chaotic dynamics might be related to voice pathology induced by the ventricular phonation. A computational model was further presented to elucidate the experimental findings.

Clinical Symptoms, Endoscopic Imaging and Stroboscopic Imaging in Patients with Vocal Fold Polyp at National ENT Hospital from August 2020 to May 2021

Vocal fold polyps are one of the most frequent benign laryngeal lesions, impacting the quality of voice of patients. This study aims to describe clinical characteristics, endoscopic and stroboscopic imaging in patients with vocal fold. The study used clinical images and histopathology to describe case series of 32 patients diagnosed with vocal fold polyps from august 2020 to May 2021. The study results show that the average age of the subjects was 42.1 ± 12.3; the most common risk factor was laryngopharyngeal reflux (71.8%); the most common symptoms were hoarseness (100%), of which moderate hoarseness was 59.4%), sore throat - 50%, vocal fatigue - 43.7%; total vhi-30 score was mostly at mild significant affect (71.9%); polyps were usually found in the mid-third of the free margin (65.6%) and vocal fold incompletely closed (100%). The results of stroboscopy show that the presence of mucosal waves was 96.9% and wave amplitude decreased by 68.8%. Taken together, hoarseness is the main symptom and the reason why patients seek medical attention and the position of the vocal fold polyps is usually in the mid-third of the free margin, affecting the anatomy and voice function of the vocal folds.
 Keywords
 Vocal fold polyp, clinical characteristics, endoscopic imaging, stroboscopic imaging, LPR.
 References
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Contribution of laryngeal size to differences between male and female voice production.

In this study we investigated the effect of sex- and age-related differences in vocal fold length, thickness, and depth on voice production in a three-dimensional vocal fold model. The results showed that the cause-effect relationships between vocal fold physiology and voice production previously identified in an adult male-like vocal fold geometry remained qualitatively the same in vocal folds with geometry representative of adult females and children. We further showed that the often-observed differences in voice production between adult males, adult females, and children can be explained by differences in length and thickness. The lower F0, higher flow rate, larger vocal fold vibration amplitude, and higher sound pressure level (SPL) in adult males as compared to adult females and children can be explained by differences in vocal fold length. In contrast, the thickness effect dominated and contributed to the larger closed quotient of vocal fold vibration, larger normalized maximum flow declination rate, and lower H1-H2 in adult males as compared to adult females and children. The effect of differences in vocal fold depth was generally small. When targeting a specific SPL, adult males experienced a lower peak vocal fold contact pressure during phonation than adult females and children.

Neutron skin thickness of Pb208, Sn116,120,124 , and Ca40 determined from reaction cross sections of He4 scattering

Background: We constructed the Kyushu chiral $g$ matrix and confirmed its reliability at $30\ensuremath{\lesssim}{E}_{\mathrm{in}}\ensuremath{\lesssim}100$ MeV and $250\ensuremath{\lesssim}{E}_{\mathrm{in}}\ensuremath{\lesssim}400$ MeV for $^{12}\mathrm{C}$ scattering. Reaction cross-section data of $^{4}\mathrm{He}$ scattering are available for some nuclides including $^{208}\mathrm{Pb}$. The PREX II collaboration reported a thick neutron skin for $^{208}\mathrm{Pb}$.Purpose: Our purpose is to deduce neutron skin thicknesses of $^{208}\mathrm{Pb}$ and some other nuclides from reaction cross sections calculated in terms of the double folding model with the $g$ matrix.Methods: We fold the $g$ matrix and densities given by mean-field calculations. To remedy the weaker constraint of the neutron sector, we renormalize densities so as to reproduce the observed cross sections.Results: We found that a $3.4%$ renormalization is necessary for $^{208}\mathrm{Pb}$. The neutron density obtained from renormalization results in ${R}_{\mathrm{skin}}=0.416\ifmmode\pm\else\textpm\fi{}0.146$ fm by confronting the precision proton radius.Conclusions: Our result is consistent with PREX II and therefore supports larger slope parameter $L$. Results for $^{40}\mathrm{Ca}$ and $^{124}\mathrm{Sn}$ are also consistent with ${R}_{\mathrm{skin}}$ deduced from other experiments. For $^{116,120}\mathrm{Sn}$ the present method gives thicker skins.