Periodic motions with impact chatters in an impact Duffing oscillator.

The periodic motions of discontinuous nonlinear dynamical systems are very difficult problems to solve in engineering and physics. Until now, except for numerical studies, one cannot find a better way to solve such problems. In fact, one still has difficulty obtaining periodic motions in continuous nonlinear dynamical systems. In this paper, a method is presented systematically for periodic motions in discontinuous nonlinear dynamical systems. The stability and grazing bifurcations of such periodic motions are studied. Such a method is presented through discussion on a periodically forced, impact Duffing oscillator. Thus, periodic motions with impact chatters in a periodically forced Duffing oscillator with one-sidewall constraint are studied. The analytical conditions for motion grazing at the boundary are developed from discontinuous dynamical systems. The impact Duffing oscillator is discretized to generate subimplicit mappings. With impact, the mapping structures are employed to construct specific impact periodic motions for an impact Duffing oscillator. The bifurcation trees of impact chatter periodic motions are achieved semi-analytically. The grazing and period-doubling bifurcations are obtained, and the grazing bifurcations are for the appearing and disappearance for an impact chatter periodic motion. The impact chatter periodic motions with and without grazing are presented for illustration of impact periodic motion complexity in the impact Duffing oscillator.

Enhancing cryo-EM structure prediction with DeepTracer and AlphaFold2 integration.

Understanding the protein structures is invaluable in various biomedical applications, such as vaccine development. Protein structure model building from experimental electron density maps is a time-consuming and labor-intensive task. To address the challenge, machine learning approaches have been proposed to automate this process. Currently, the majority of the experimental maps in the database lack atomic resolution features, making it challenging for machine learning-based methods to precisely determine protein structures from cryogenic electron microscopy density maps. On the other hand, protein structure prediction methods, such as AlphaFold2, leverage evolutionary information from protein sequences and have recently achieved groundbreaking accuracy. However, these methods often require manual refinement, which is labor intensive and time consuming. In this study, we present DeepTracer-Refine, an automated method that refines AlphaFold predicted structures by aligning them to DeepTracers modeled structure. Our method was evaluated on 39 multi-domain proteins and we improved the average residue coverage from 78.2 to 90.0% and average local Distance Difference Test score from 0.67 to 0.71. We also compared DeepTracer-Refine with Phenixs AlphaFold refinement and demonstrated that our method not only performs better when the initial AlphaFold model is less precise but also surpasses Phenix in run-time performance.

Limit cycles and homoclinic networks in two-dimensional polynomial systems.

In this paper, the properties of equilibriums in planar polynomial dynamical systems are studied. The homoclinic networks of sources, sinks, and saddles in self-univariate polynomial systems are discussed, and the numbers of sources, sinks, and saddles are determined through a theorem, and the first integral manifolds are determined. The corresponding proof of the theorem is completed, and a few illustrations of networks for source, sinks, and saddles are presented for a better understanding of the homoclinic networks. Such homoclinic networks are without any centers even if the networks are separated by the homoclinic orbits. The homoclinic networks of positive and negative saddles with clockwise and counterclockwise limit cycles in crossing-univariate polynomial systems are studied secondly, and the numbers of saddles and centers are determined through a theorem, and the first integral manifolds are determined through polynomial functions. The corresponding proof of the theorem is given, and a few illustrations of networks of saddles and centers are given to show the corresponding geometric structures. Such homoclinic networks of saddles and centers are without any sources and sinks. Since the maximum equilibriums for such two types of planar polynomial systems with the same degrees are discussed, the maximum centers and saddles should be obtained, and maximum sinks, sources, and saddles should be achieved. This paper may provide a different way to determine limit cycles in the Hilbert 16th problem.

Constructed complex motions and chaos.

Constructed motions and dynamic topology are new trends in solving nonlinear systems or system interactions. In nonlinear engineering, it is significant to achieve specific complex motions to satisfy expected dynamical behaviors (e.g., nonlinear motions, singularities, bifurcations, chaos, etc.), and complex motion application and control. To achieve such expected motions and global dynamical behaviors, mapping dynamics, constructed networks, random/discontinuous dynamic theorems, etc., are applied to quantitatively determine the complex motions. These theories adopt the symbolic dynamic abstracts and topological structures with nonlinear dynamics to investigate constructed complex motions to satisfy expected dynamical behaviors.

Period-3 motions to chaos in a periodically forced nonlinear-spring pendulum.

In this paper, the complete bifurcation dynamics of period-3 motions to chaos are obtained semi-analytically through the implicit mapping method. Such an implicit mapping method employs discrete implicit maps to construct mapping structures of periodic motions to determine complex periodic motions. Analytical bifurcation trees of period-3 motions to chaos are determined through nonlinear algebraic equations generated through the discrete implicit maps, and the corresponding stability and bifurcations of periodic motions are achieved through eigenvalue analysis. To study the periodic motion complexity, harmonic amplitudes varying with excitation amplitudes are presented. Once more, significant harmonic terms are involved in periodic motions, and such periodic motions will be more complex. To illustrate periodic motion complexity, numerical and analytical solutions of periodic motions are presented for comparison, and the corresponding harmonic amplitudes and phases are also presented for such periodic motions in the bifurcation trees of period-3 motions to chaos. Similarly, other higher-order periodic motions and bifurcation dynamics for the nonlinear spring pendulum can be determined. The methods and analysis presented herein can be applied for other nonlinear dynamical systems.

Periodic motions and homoclinic orbits in a discontinuous dynamical system on a single domain with multiple vector fields.

In this paper, periodic motions and homoclinic orbits in a discontinuous dynamical system on a single domain with two vector fields are discussed. Constructing periodic motions and homoclinic orbits in discontinuous dynamical systems is very significant in mathematics and engineering applications, and how to construct periodic motions and homoclinic orbits is a central issue in discontinuous dynamical systems. Herein, how to construct periodic motions and homoclinic orbits is presented through studying a simple discontinuous dynamical system on a domain confined by two prescribed energies. The simple discontinuous dynamical system has energy-increasing and energy-decreasing vector fields. Based on the two vector fields and the corresponding switching rules, periodic motions and homoclinic orbits in such a simple discontinuous dynamical system are studied. The analytical conditions of bouncing, grazing, and sliding motions at the two energy boundaries are presented first. Periodic motions and homoclinic orbits in such a discontinuous dynamical system are determined through the specific mapping structures, and the corresponding stability is also presented. Numerical illustrations of periodic motions and homoclinic orbits are given for constructed complex motions. Through this study, using discontinuous dynamical systems, one can construct specific complex motions for engineering applications, and the corresponding mathematical methods and computational strategies can be developed.

Nonlinear piezoelectric energy harvesting induced through the Duffing oscillator.

In this paper, nonlinear piezoelectric energy harvesting induced by a Duffing oscillator is studied, and the bifurcation trees of period-1 motions to chaos for such a piezoelectric energy-harvesting system are obtained analytically. Distributed-parameter electromechanical modeling of a piezoelectric energy harvester is presented first, and the electromechanically coupled circuit equation excited by infinitely many vibration modes is developed. The governing electromechanical equations are reduced to ordinary differential equations in modal coordinates, and eventually an infinite set of algebraic equations is obtained for the complex modal vibration responses and the complex voltage responses of the energy harvester beam. One single mode case is considered in this paper, and periodic motions with bifurcation trees are obtained through an implicit discrete mapping method. The frequency-amplitude characteristics of periodic motions are obtained for the nonlinear piezoelectric energy-harvesting systems, which provide a better understanding of where and how to achieve the best energy harvesting. This study describes about how the nonlinear oscillator induces piezoelectric energy harvesting through a beam system. The nonlinear piezoelectric energy harvesting is presented through a nonlinear oscillator. Due to the nonlinear oscillator, chaotic piezoelectric energy-harvesting states can get more energy compared to the linear piezoelectric energy-harvesting system.

On an origami structure of period-1 motions to homoclinic orbits in the Rössler system.

In this paper, an origami structure of period-1 motions to spiral homoclinic orbits in parameter space is presented for the Rössler system. The edge folds of the origami structure are generated by the saddle-node bifurcations. For each edge, there are two layers to form the origami structure. On one layer of the origami structure, there is a pair of period-doubling bifurcations inducing periodic motions from period-1 to period-2n motions (n=1,2,…,∞). On such a layer, the unstable period-1 motion goes to the homoclinic orbits with a mapping eigenvalue approaching negative infinity. However, on the corresponding adjacent layers, no period-doubling bifurcations exist, and the unstable period-1 motion goes to the homoclinic orbit with a mapping eigenvalue approaching positive infinity. To determine the origami structure of the period-1 motions to homoclinic orbits, the implicit map of the Rössler system is developed through the discretization of the corresponding differential equations. The Poincaré mapping section can be selected arbitrarily. Before construction of the origami structure, the bifurcation diagram of periodic motions varying with one parameter is developed, and trajectories of stable periodic motions on the bifurcation diagram to homoclinic orbits are illustrated. Finally, the origami structures of period-1 motions to homoclinic orbits are developed through a few layers. This study provides the mathematical mechanisms of period-1 motions to homoclinic orbits, which help one better understand the complexity of periodic motions near the corresponding homoclinic orbit. There are two types of infinitely many homoclinic orbits in the Rössler system, and the corresponding mapping structures of the homoclinic orbits possess positive and negative infinity large eigenvalues. Such infinitely many homoclinic orbits are induced through unstable periodic motions with positive and negative eigenvalues accordingly.

On infinite homoclinic orbits induced by unstable periodic orbits in the Lorenz system.

In this paper, infinite homoclinic orbits existing in the Lorenz system are analytically presented. Such homoclinic orbits are induced by unstable periodic orbits on bifurcation trees through period-doubling cascades. Each unstable periodic orbit ends at its corresponding homoclinic orbit. Traditional computational methods cannot obtain homoclinic orbits from the corresponding unstable periodic orbits. This is because unstable periodic orbits in the Lorenz system cannot be achieved in numerical simulations. Herein, the stable and unstable periodic motions to chaos on the period-doubling cascaded bifurcation trees are determined through a discrete mapping method. The corresponding homoclinic orbits induced by the unstable periodic orbits are predicted analytically. A period-doubling bifurcation tree of period-1, period-2, and period-4 motions are generated as an example. The homoclinic orbits relative to unstable period-1, period-2, and period-4 motions are determined. Illustrations of homoclinic orbits and periodic orbits are given. This study presents how to determine infinite homoclinic orbits through unstable periodic orbits in three-dimensional or higher-dimensional nonlinear systems.

Challenges in the phenotypic characterisation of patients in genetic studies of coronary artery disease.

Coronary artery disease and acute myocardial infarction are complex traits in which there has been recent research to identify the principal genes that engender susceptibility or provide protection. Although there has been exceptional progress in the technology, which now allows genotyping of hundreds of thousands of single-nucleotide polymorphisms in each individual, there remains a pattern of inconsistency in the studies performed to date, in part owing to the difficulties in defining cases and controls. In this paper, salient issues to facilitate research in this important field are reviewed.

Imaging microvascular obstruction and its clinical significance following acute myocardial infarction.

Obstruction of the coronary microvasculature contributes to the pathophysiology of MI and adversely affects post-MI recovery. This "no-reflow" phenomenon resulting from microvascular obstruction is an indicator of lack of adequate tissue perfusion within the infarcted myocardium, even after restoration of epicardial blood flow. Regions of microvascular obstruction can be detected and quantifed because of rapid advances in and refinement of imaging technologies over the past decade. This article focuses on the non-invasive imaging modalities used to assess MO, discusses the prognostic implications of MO, and briefly addresses strategies for reducing MO.

High-throughput single-nucleotide polymorphisms genotyping: TaqMan assay and pyrosequencing assay.

Single-nucleotide polymorphisms (SNPs) are DNA sequence variations that occur at a single base in the genome sequence. SNPs are valuable markers for identifying genes responsible for susceptibility to common diseases, and in some cases, they are the causes of human diseases. A genetic study of a complex disease usually involves a case-control association study that requires genotyping of a large number of SNPs in hundreds of patients (cases) and matched controls. A significant difference of the allele frequency or genotypic frequency of a SNP between the two populations is considered to be the evidence for the association between the SNP and disease. A key to a fast and effective case-control association study requires high-throughput genotyping of SNPs. Two assays-the TaqMan SNP genotyping assay and the pyrosequencing assay-have been developed for this purpose and proven to be particularly useful. Here, we present the operative protocol, clarify the key technical issues, and highlight certain cautionary notes for high throughput SNP genotyping using TaqMan and pyrosequencing assays.