Exit Path Research Articles

Quasi-threshold phenomenon in noise-driven Higgins model

The quasi-threshold phenomenon in Higgins model with mono-stability driven by Gaussian white noise is investigated. The initial excitation phase is identified as escaping event with a specific trajectory defined as the quasi-threshold. In the limit of weak noise, a group of differential equations governing the optimal exit path, quasi-potential and exponential prefactor are deduced via WKB approximation. Results show that the optimal path approaches the quasi-threshold with a nearly tangent way and almost follows the deterministic flow subsequently in the quasi-potential plateau, making it analogous to the bistable system. Numerical experiments verify not only the results of the optimal path but also the ones of the optimal fluctuational forces. Then the difference between the practical exit location and the position with minimal quasi-potential is also revealed by including the exponential prefactor into the expression of exit location distribution. Finally, the mean first passage time (MFPT) is evaluated theoretically with the secondary-order-approximation taken into consideration. These findings and computations shed light on exploring underlying qualitative mechanism and quantitative feature of excitation behaviors in biological systems.

It's in the loop: shared sub-surface foot kinematics in birds and other dinosaurs shed light on a new dimension of fossil track diversity.

The feet of ground-dwelling birds retain many features of their dinosaurian ancestry. Experiments with living species offer insights into the complex interplay among anatomy, kinematics and substrate during the formation of Mesozoic footprints. However, a key aspect of the track-making process, sub-surface foot movement, is hindered by substrate opacity. Here, we use biplanar X-rays to image guineafowl walking through radiolucent substrates of different consistency (solid, dry granular, firm to semi-liquid muds). Despite substantial kinematic variation, the foot consistently moves in a looping pattern below ground. As the foot sinks and then withdraws, the claws of the three main toes create entry and exit paths in different locations. Sampling these paths at incremental horizons captures two-dimensional features just as fossil tracks do, allowing depth-based zones to be characterized by the presence and relative position of digit impressions. Examination of deep, penetrative tracks from the Early Jurassic confirms that bipeds had an equivalent looping response to soft substrates approximately 200 Ma. Our integration of extant and extinct evidence demonstrates the influence of substrate properties on sinking depth and sub-surface foot motion, both of which are significant sources of track variation in the fossil record of dinosaurs.

Aerodynamic study of paratrooper models used in the C-130 H/J personnel drop operations

The goal of this study is to conduct time-accurate simulations of several paratrooper models exiting the troop door of a C-130 aircraft. Solutions are calculated using HPCMP CREATETM-AV Kestrel software. Both the second-order, unstructured finite-volume solver of kCFD and the structured Cartesian finite-volume solver of SAMAir, which enables near-body/off-body calculations and adaptive mesh refinement, are used. The objective of this article is to analyze the effects of the unsteady flow field around the troop door on representative paratrooper models positioned at different locations and orientations. The predictions are presented in terms of integrated forces and moments in both time and frequency domains. Averaged forces/moments are reported as well. Vortex shedding frequency with maximum power density is predicted from forces or air velocity measurements at tap points behind the models. The contribution of primitive geometric elements (body, arms, and orientation) to the wake shedding frequencies are detailed, and results include validation of predicted vortex shedding frequency for a cylinder of aspect ratio 10 (length to diameter) with available experimental data. The results show that the adaptive mesh refinement aids in better resolution of the wake structure and better agreement with measured data. When the models exit the C-130 troop doors, the wind deflectors significantly reduce the rearward aerodynamic forces acting on the models compared with free-stream/stand-alone models. However, the flow field around the door changes the roll and yaw moments and the side force (force in the spanwise direction) as compared with the stand-alone model. Finally, the results document the aerodynamic forces and moments as functions of the static position and orientation of the paratrooper model relative to the door. The approach used and results of these simulations form a baseline for future simulation enhancements, which include calculating the exit path of the paratrooper relative to the aircraft, static line jumps, and subsequent parachute deployment.

Most probable dynamics of stochastic dynamical systems with exponentially light jump fluctuations.

The emergence of the exit events from a bounded domain containing a stable fixed point induced by non-Gaussian Lévy fluctuations plays a pivotal role in practical physical systems. In the limit of weak noise, we develop a Hamiltonian formalism under the Lévy fluctuations with exponentially light jumps for one- and two-dimensional stochastic dynamical systems. This formalism is based on a recently proved large deviation principle for dynamical systems under non-Gaussian Lévy perturbations. We demonstrate how to compute the most probable exit path and the quasi-potential by several examples. Meanwhile, we explore the impacts of the jump measure on the quasi-potential quantitatively and on the most probable exit path qualitatively. Results show that the quasi-potential can be well estimated by an approximate analytical expression. Moreover, we discover that although the most probable exit paths are analogous to the Gaussian case for the isotropic noise, the anisotropic noise leads to significant changes in the structure of the exit paths. These findings shed light on the underlying qualitative mechanism and quantitative feature of the exit phenomenon induced by non-Gaussian noise.

Exit from equilibrium in coordination games under probit choice

We consider a model of stochastic evolution under the probit choice rule. In the small noise double limit, where first the noise level in agents' decisions is taken to zero, and then the population size to infinity, escape from and transitions between equilibria can be described in terms of solutions to continuous optimal control problems. We use results from optimal control theory to solve the exit cost problem. This is used to determine the most likely exit paths from the initial basin of attraction and also to assess the expected time until the evolutionary process leaves the basin of attraction of a stable equilibrium in a class of three-strategy coordination games.

Eliminating occluded voids in additive manufacturing design via a projection-based topology optimization scheme

Design for additive manufacturing (AM) requires knowledge of the constraints associated with your targeted AM process. One important design concern is the unintentional trapping of parasitic mass in occluded void geometries with either uncured or non-solidified material, or in some cases, sacrificial support material. These occluded features create the need to physically alter the optimal topology to remove the material. In this work, a projection-based topology optimization design formulation is proposed to eliminate occluded void topological features in optimal AM designs. The algorithm is based on the combination and enhancement of two existing algorithms: a projection-based, overhang-constrained algorithm to design self-supporting structures in AM, and a void projection algorithm to design topologies through control of the void phase. The combined algorithm results in topologies with void regions that always possess an exit path to predefined outer surfaces – i.e. drainage pathways. Solutions are first demonstrated in two dimensions, with increasing design freedom allowed through algorithm enhancements. The algorithm is then adapted to 3D, adopting a multi-phase TO approach to not only regain control of the solid phase length scale, but also to drive toward superior performing topologies with minimal impact on the part performance.

Crowd Evacuation Behaviour Modeling and Simulation in 3D Platform

Crowd simulation is an active research domain and is crucial for simulating crowd behaviour in certain condition such as normal or panic situation. The simulation is to show the interaction between the individual in a crowd. Nowadays, there are many kinds of scenarios as well as simulation softwares that can be adapted to simulate a crowd simulation such as during emergency situation e.g. building evacuation. Crowd simulation in three-dimensional platform is fairly important in order to have a more realistic looks and movement of the crowd in one particular environment. The evacuation simulation is useful for the crowd in one confinement to seek for a safe exit path in shortest time possible and thus increase the occupant’s safety. The evacuation time is said to be in safe condition if all the evacuees successfully can get through the exit in minimal time. To aid in minimal exit time, the concept of faster-is-slower (bottleneck) must be solved as it can lead to more waiting time or delay during evacuation process. In this paper, it will discuss about the crowd simulation behavior, crowd simulation based on agent-based model, existing crowd simulation tools and the result of simulating the three-dimensional (3D) crowd evacuation time based on a number of exits variation in panic situation. The tools used to carry out the experiment is Anylogic software whereby the results show that it adheres to shorter evacuation time when the number of exit increases. The 3D layout design was following the original layout the faculty’s lower ground floor where the classrooms are mostly resided. The simulation is useful in order to estimate of evacuation time with different total number of exits to alleviate the faster-is-slower effect in case of any emergency situation happens at the faculty building.

Crystallographic and cryogenic electron microscopic structures and enzymatic characterization of sulfur oxygenase reductase from Sulfurisphaera tokodaii

Sulfur oxygenase reductases (SORs) are present in thermophilic and mesophilic archaea and bacteria, and catalyze oxygen-dependent oxygenation and disproportionation of elemental sulfur. SOR has a hollow, spherical homo-24-mer structure and reactions take place at active sites inside the chamber. The crystal structures of SORs from Acidianus species have been reported. However, the states of the active site components (mononuclear iron and cysteines) and the entry and exit paths of the substrate and products are still in dispute. Here, we report the biochemical and structural characterizations of SORs from the thermoacidophilic archaeon Sulfurisphaera tokodaii (StSOR) and present high-resolution structures determined by X-ray crystallography and cryogenic electron microscopy (cryo-EM). The crystal structure of StSOR was determined at 1.73 Å resolution. At the catalytic center, iron is ligated to His86, His90, Glu114, and two water molecules. Three conserved cysteines in the cavity are located 9.5–13 Å from the iron and were observed as free thiol forms. A mutational analysis indicated that the iron and one of the cysteines (Cys31) were essential for both activities. The cryo-EM structure was determined at 2.24 Å resolution using an instrument operating at 200 kV. The two structures determined by different methodologies showed similar main chain traces, but the maps exhibited different features at catalytically important components. A possible role of StSOR in the sulfur metabolism of S. tokodaii (an obligate aerobe) is discussed based on this study. Given the high resolution achieved in this study, StSOR was shown to be a good benchmark sample for cryo-EM.

Structure, Thermodynamics, and Kinetics of Plinabulin Binding to Two Tubulin Isotypes

Summary αβ-Tubulin is a validated target for anticancer drug discovery, and molecules binding to this protein are used to treat several types of tumors. Here, we report on a combined X-ray crystallography and molecular dynamics approach to study drug binding within the colchicine site of αβ-tubulin, focusing on plinabulin, an agent currently in phase 3 clinical testing for the treatment of cancer and chemotherapy-induced neutropenia. We found that plinabulin is more persistently bound to the colchicine site of βII- compared to βIII-tubulin, allowing for a prediction of isotype-expression-dependent drug sensitivity. Additionally, computational residence time and exit paths from the βII-tubulin were compared between plinabulin and two other compounds, colchicine and combretastatin-A4. The former displayed the highest residence time, followed by plinabulin and then distantly by combretastatin-A4. Our combined experimental and computational protocol could help to investigate anti-tubulin drugs, improving our understanding of their mechanism of action, residence time, and tubulin isotype selectivity.

Percolation Behavior in Catalytic Porous Material

Proper water management in Polymer Exchange Membrane (PEM) fuel cell is important to achieve high performance. Understanding the percolation of the produced water at the cathode catalyst layer (CL), is critical for any robust water management technique. The CL consists of a complex structure to allow reactants to pass through and reach the reaction catalyst site. The complex structure is made by a support structure (mostly carbon) that allows the transport of electrons, an ionomer that conducts protons, and voids that have the double role of oxygen breathing and exit paths for the generated water. In this work, a pseudo-Hele–Shaw experimental setup is used to investigate immiscible fluid displacement inside the CL under controlled conditions. Since water can be retained by ionomer, making it swell and caused a shift in the pore size distribution, fluor-inert is used as a working fluid. The evolution of percolation pressure and the projected area of the injected fluid are recorded simultaneously. Preliminary results show a high consistency in the measured data at high flow rate percolation. However, at low flow rate there is some variation in the data due to relative humidity effect. The experimental data is considered as an input to the (Ce-t^*) scale. This scaling has been previously developed (Medici & Allen, 2011) to study two phase flow in thin porous layers. The dimensionless energy scale (Ce) based on the ratio between the injected and dissipated energies. The other dimensionless time scale (t^*) is arises from the important of the time of percolation, where in capillary regime is in order of hours while in stable displacement is in order of minutes, so it characterizes the relative effects of viscous and capillary effect. This scaling collapses transient pressure and saturation to a linear, non-dimensional and unique correlation for each material.

Percolation Behavior in Catalytic Porous Material

Proper water management in Polymer Exchange Membrane (PEM) fuel cell is important to achieve high performance. Understanding the percolation of the produced water at the cathode catalyst layer (CL), is critical for any robust water management technique. The CL consists of a complex structure to allow reactants to pass through and reach the reaction catalyst site. The complex structure is made by a support structure (mostly carbon) that allows the transport of electrons, an ionomer that conducts protons, and voids that have the double role of oxygen breathing and exit paths for the generated water. In this work, a pseudo-Hele–Shaw experimental setup is used to investigate immiscible fluid displacement inside the CL under controlled conditions. Since water can be retained by ionomer, making it swell and caused a shift in the pore size distribution, fluor-inert is used as a working fluid. The evolution of percolation pressure and the projected area of the injected fluid are recorded simultaneously.

Understanding School Principal Attrition and Mobility Through Hierarchical Generalized Linear Modeling

Despite a growing body of turnover literature, much remains unknown about the factors predicting career transitional behaviors of school principals. To bridge this gap, we examined variations in principal, school, and district characteristics influencing administrator leaver and mover behaviors, using Hierarchical Generalized Linear Modeling. Our findings revealed that class size, support staff, parental involvement, teacher incentives, unionization, and many other district-level policies offset turnover, thereby contributing to retention. Furthermore, predictors of principal mover behavior differed from those of principal leaver behavior, suggesting that different forms of exit paths may need different policy tools to improve retention.

Case of congenital adrenocortical cancer

The article presents a unique clinical observation of adrenocortical cancer (ACC) in a newborn baby, whose mother suffered from a recurrent form of maxillary fibrosarcoma and had a burdened obstetric and gynecological history, but was not examined by a geneticist. Complications of ACC in the presented patient were secondary hypertrophic cardiomyopathy with obstruction of the exit paths of both ventricles, Itsenko– Cushing syndrome. Despite the surgical treatment carried out according to vital indications (tumoradinectomy on the right with hormonal support with a Solu-Cortef), the child died during the progression of multiple organ failure and sepsis.

BUILDING A STABLE SYSTEM OF FOREIGN ECONOMIC RELATIONS BETWEEN THE CZECH REPUBLIC AND SLOVAKIA: EXPERIENCE FOR

В статті автор досліджує процеси побудови та подальшої трансформації системи міждержавного співробітництва та стабільного розвитку зовнішньоекономічної співпраці Чеської і Словацької республік, здійснює аналіз особливостей економічного партнерства між складовими частинами колись єдиної держави, «мирне розлучення» якої дало поштовх для розвитку цілого ряду країн регіону Центральної та Східної Європи і України, зокрема. Відзначається, що незалежні Чехія і Словаччина вимушені були фактично вперше формувати самостійну систему зовнішньоекономічної політики і міждержавних економічних зв'язків. Втім, наростання відмінних рис у чеському і словацькому варіанті постсоціалістичного реформування після 1993 року лише незначним чином торкнулося зовнішньоекономічної сфери. Нові ринкові принципи зовнішньоекономічної діяльності були запроваджені ще в ході «клаусівських» реформ у рамках федерації. Чеська Республіка і Словаччина, які в минулому входили до єдиного економічного комплексу, пройшли тривалий шлях трансформації від соціалістичної системи планової економіки до ринкової моделі господарювання. Активна економічна позиція і спрямованість на європейську та євроатлантичну інтеграцію призвела до очікуваних результатів – значне економічне зростання, контрольований рівень інфляції. Разом із тим, система зовнішньоекономічного співробітництва та торгово-економічні відносини, як окремо двох країн так і чесько-словацьке партнерство, зазнали деяких суттєвих зрушень. Після проведення комплексу економічної діагностики виявлені найбільш значимі результати для Словаччини. Після вступу до зони євро Словаччина отримала надійний базис для сталого розвитку власної економічної системи. Ця подія співпала із загостренням негативного впливу світової фінансово-економічної кризи на економіку Словаччини та стала одним із факторів оживлення економічного росту. Також автор відмічає той факт, що в умовах створення біля кордонів України інтегрованої ринкової зони з режимом вільної торгівлі, українська держава не могла залишатися осторонь цієї регіональної економічної інтеграції. Україна в середині 1990-х – початку 2000-х років прагнула стати повноправним членом «європейської економічної родини». Її бажання на той час підтримували майже всі держави Центральної та Східної Європи.

Minimum Action Path Theory Reveals the Details of Stochastic Transitions Out of Oscillatory States.

Cell state determination is the outcome of intrinsically stochastic biochemical reactions. Transitions between such states are studied as noise-driven escape problems in the chemical species space. Escape can occur via multiple possible multidimensional paths, with probabilities depending nonlocally on the noise. Here we characterize the escape from an oscillatory biochemical state by minimizing the Freidlin-Wentzell action, deriving from it the stochastic spiral exit path from the limit cycle. We also use the minimized action to infer the escape time probability density function.

Quantitative birefringence microscopy with collinearly propagating orthogonally polarized beams.

Full-field evaluation of spatially varying birefringence is realized by allowing two mutually orthogonally polarized collinearly propagating laser beams to be incident on a birefringent sample. This is achieved by use of a modified Sagnac interferometer. A half-wave plate is placed in the exit path of the interferometer to adjust the polarizations of the incident beams as required. Amplitude components of the light emerging from the birefringent object are then selected and/or combined by a polarizer, and intensities for required orientation of the half-wave plate and the analyzer are digitally recorded. It is shown that a maximum of four frames of intensity data is sufficient for complete evaluation of birefringence. The proposed technique is aimed towards birefringence measurements in microscopic biological specimens where the magnitude of retardation lies in the range of 0-π radians. Simulated and experimental results are presented.

Application of Labor Laws and Other Compliances in Readymade Garment Industry of Bangladesh

Although, the economy of Bangladesh is primarily dependent on agriculture, Readymade Garment (RMG) industry has emerged as the largest earner foreign currency of Bangladesh in recent years. More than 75% of foreign earnings are coming through export from this very important sector of Bangladesh. In study of Islam & Chowdhuri, [1] presently more than four million workers are working in 4,500 RMG companies of Bangladesh in which 90% are illiterate women who are from the rural areas of the country. The policymakers and the employers of this sector claim that the growth of garment sector has helped employing a huge number of rural women that has subsequently developed their socioeconomic. But, it is a concern of the national and internal observers that the compliances like factory laws, industrial relations laws, employment laws, payment of wages laws, ILO standards, ethics applied in this sector are hardly followed by the RMG companies that make the lives of the workers very misery. Sometimes, the female workers are exploited by employing more hours a day without the payment of overtime by capitalizing their illiteracy and submissiveness. Hence, this paper aims at identifying the level of application of the labor laws and the compliances in RMG industry of Bangladesh that is the only protective measures of the large number of female workers of this sector of Bangladesh. A total of 238 workers of this sector were interviewed in this study with a structured questionnaire. Multivariate analysis techniques such as, Factor Analysis and Multiple Regression Analysis were used to analyze the data. Results show that in case of measures for protecting sexual harassment there is a severe problem of the use of the labor laws in this sector followed by physical movement and access control, exit and access path of the company, working hours, and counseling arrangements in the company. This study suggests that the readymade garment companies should address the sexual harassment issue seriously so that the workers will feel safe at their work. They also should focus more on the safety issues, working hours, and counseling of the workers in order to make the working environment more favorable to the workers.

Steered molecular dynamics for studying ligand unbinding of ecdysone receptor

Ecdysone receptor (EcR) is an important target for pesticide design. Ligand binding regulates EcR transcriptional activity similar to other nuclear receptors; however, the pathways by which ligands enter and leave the EcR remain poorly understood. Here, we performed computational studies to identify unbinding pathways of an ecdysone agonist [the selective ecdysone agonist, BYI06830] from the EcR ligand binding domain (EcR LBD). BYI06830 can dissociate from EcR LBD via four different pathways with little effect on receptor structure. By comparing the potential of mean force (PMF) of four pathways, path 2 was considered to be the most likely exit path for BYI06830, which was located in the cleft formed by the H3-H4 loop, H6-H7 loop, and the H11 C-terminus. Furthermore, structural features along path 2 were analyzed and the structural snapshots of the metastable and transition states were isolated to illustrate the unbinding mechanism of ecdysone agonist from EcR LBD.

Transcription machinery remains steadfast

Transcription Eukaryotic transcription of mRNA is a multistep process mediated by RNA polymerase II (Pol II). Pol II combines with several other factors to form an elongation complex that promotes transcription elongation. Ehara et al. determined the high-resolution structure of the elongation complex by means of x-ray crystallography and cryo-electron microscopy (see the Perspective by Fouqueau and Werner). Multiple elongation factors are distributed on a wide surface of Pol II and establish an RNA exit path and DNA entry or exit tunnels, which facilitate nascent transcript transfer and DNA unwinding or rewinding. The Pol II elongation complex thus adopts a stable architecture suitable for processive transcription. Science , this issue p. [921][1]; see also p. [871][2] [1]: /lookup/doi/10.1126/science.aan8552 [2]: /lookup/doi/10.1126/science.aao4754

Structure of the complete elongation complex of RNA polymerase II with basal factors.

In the early stage of transcription, eukaryotic RNA polymerase II (Pol II) exchanges initiation factors with elongation factors to form an elongation complex for processive transcription. Here we report the structure of the Pol II elongation complex bound with the basal elongation factors Spt4/5, Elf1, and TFIIS. Spt4/5 (the Spt4/Spt5 complex) and Elf1 modify a wide area of the Pol II surface. Elf1 bridges the Pol II central cleft, completing a "DNA entry tunnel" for downstream DNA. Spt4 and the Spt5 NGN and KOW1 domains encircle the upstream DNA, constituting a "DNA exit tunnel." The Spt5 KOW4 and KOW5 domains augment the "RNA exit tunnel," directing the exiting nascent RNA. Thus, the elongation complex establishes a completely different transcription and regulation platform from that of the initiation complexes.