Intermediate Configuration Research Articles

Numerical Method for Solving the Problem of Thermomechanics of Polymeric Environment in Conditions of Phase Transition

A methodology and a numerical algorithm of solving boundary problems of mechanics of deformable crystallizing elastic polymer media have been developed. A class of problems describing processes taking place in polymer products during their manufacturing is considered. Due to the significance of shrinking deformations the problem is considered within finite deformations theory. Constitutive relations are built on base of Peng-Landel potential. A ‘weak’ variation problem statement based on Galerkin approach is used. The offered algorithm is based on linearization methodology when small deformations are applied to finite ones. Deformation process is considered as a sequence of transitions through intermediate configurations. This approach makes possible to bring the received solution to the sequence of linearized boundary problems for which effective numerical algorithms have been designed. Numerical procedure is based on the technology of finite element method. Increments of displacements on the considered time step are taken to be nodal unknowns. The offered algorithm is applied to solution of the problem concerning the polyethylene pipe deformation during its manufacturing. Main advantages of the proposed algorithm have been defined.

β-sheet-like formation during the mechanical unfolding of prion protein.

Single molecule experiments and simulations have been widely used to characterize the unfolding and folding pathways of different proteins. However, with few exceptions, these tools have not been applied to study prion protein, PrP(C), whose misfolded form PrP(Sc) can induce a group of fatal neurodegenerative diseases. Here, we apply novel atomistic modeling based on potential energy surface exploration to study the constant force unfolding of human PrP at time scales inaccessible with standard molecular dynamics. We demonstrate for forces around 100 pN, prion forms a stable, three-stranded β-sheet-like intermediate configuration containing residues 155-214 with a lifetime exceeding hundreds of nanoseconds. A mutant without the disulfide bridge shows lower stability during the unfolding process but still forms the three-stranded structure. The simulations thus not only show the atomistic details of the mechanically induced structural conversion from the native α-helical structure to the β-rich-like form but also lend support to the structural theory that there is a core of the recombinant PrP amyloid, a misfolded form reported to induce transmissible disease, mapping to C-terminal residues ≈160-220.

Optical spike-timing-dependent plasticity with weight-dependent learning window and reward modulation.

Optical spike-timing-dependent plasticity (STDP) synapses form the basis of learning in photonic neuromorphic system. In biological neural systems, STDP synapses generally have multiplicative boundary mechanisms, and can be modulated by a third factor such as dopamine. Analogously, we introduce a third factor into optical STDP: The current-injection of semiconductor optical amplifiers can be modified in an adaptive way according to local or global feedback signals. The local one is present synaptic weight, which elicits an optical weight-dependent STDP, while the global one is a reward signal. We demonstrate that the optical weight-dependent STDP can emulate the behavior of biological STDP synapses more closely, and can be seen as an intermediate configuration between additive and multiplicative STDP, which balances stability and competition among synapses. Simulation studies with scalable photonic neurons further show that optical STDP with reward modulation enables reward-based reinforcement learning.

Auditable versioned data storage outsourcing

Auditability is crucial for data outsourcing, facilitating accountability and identifying data loss or corruption incidents in a timely manner, reducing in turn the risks from such losses. In recent years, in synch with the growing trend of outsourcing, a lot of progress has been made in designing probabilistic (for efficiency) provable data possession (PDP) schemes. However, even the recent and advanced PDP solutions that do deal with dynamic data, do so in a limited manner, and for only the latest version of the data. A naive solution treating different versions in isolation would work, but leads to tremendous overheads, and is undesirable. In this paper, we present algorithms to achieve full persistence (all intermediate configurations are preserved and are modifiable) for an optimized skip list (known as FlexList) so that versioned data can be audited. The proposed scheme provides deduplication at the level of logical, variable sized blocks, such that only the altered parts of the different versions are kept, while the persistent data-structure facilitates access (read) of any arbitrary version with the same storage and process efficiency that state-of-the-art dynamic PDP solutions provide for only the current version, while commit (write) operations incur around 5% additional time. Furthermore, the time overhead for auditing arbitrary versions in addition to the latest version is imperceptible even on a low-end server. Additionally, the application of our approach opens up the possibility to naturally support block level deduplication. While a naive solution to audit versions would copy the whole data and the data structure for each version, our solution utilizes storage space amounting very close to the most efficient delta-based solutions. Accordingly, we explore how the proposed data structure benefits the system with block level deduplication besides adding auditability property, and how it can be integrated with a state-of-the-art versioning system (Git), and in the process scale the storage efficiency of Git, and thus help scale the size of data to be stored in Git, without compromising the retrieval efficiency of arbitrary versions.

Mapping Structural Changes in Electrode Materials: Application of the Hybrid Eigenvector-Following Density Functional Theory (DFT) Method to Layered Li0.5MnO2

The migration mechanism associated with the initial layered-to-spinel transformation of partially delithiated layered LiMnO2 was studied using hybrid eigenvector-following coupled with density functional theory. The initial part of the transformation mechanism of Li0.5MnO2 involves the migration of Li into both octahedral and tetrahedral local minima within the layered structure. The next stage of the transformation process involves the migration of Mn and was found to occur through several local minima, including an intermediate square pyramidal MnO5 configuration and an independent Mn3+ to Mn2+ charge-transfer process. The migration pathways were found to be significantly affected by the size of the supercell used and the inclusion of a Hubbard U parameter in the DFT functional. The transition state searching methodology described should be useful for studying the structural rearrangements that can occur in electrode materials during battery cycling, and more generally, ionic and electronic transport phenomena in a wide range of energy materials.

Monolayer-Protected Anionic Au Nanoparticles Walk into Lipid Membranes Step by Step

The design of ligand-protected metal nanoparticles (NPs) with biomedical applications relies on the understanding, at the molecular level, of their interactions with cell membranes. Here we study, via unbiased coarse grained molecular dynamics simulations, the kinetics and the thermodynamics of the interaction between anionic ligand-protected gold NPs and model lipid membranes. The NP–membrane interaction is a three-step process: electrostatics-driven adhesion to the membrane surface, hydrophobic contact and final embedding in the membrane core via anchoring of the charged ligands to both membrane leaflets. Our free energy calculations show that anchoring is highly favorable and not reversible. Furthermore, we show that the interaction pathway of NPs with random surface arrangement of anionic and hydrophobic ligands is characterized by two metastable configurations: adsorbed at the membrane surface, and membrane-embedded. Patched ligand arrangements, instead, lead to the stabilization of a third, intermediate metastable configuration, resulting in a much slower kinetics of interaction with the membrane.

Design, motion planning and control of a reconfigurable hybrid structure

Compared to traditional fixed-shaped structures, reconfigurable structures may provide various advantages with regard to space utilization, building form optimization and energy efficiency. The purpose of this study is to present the development and kinematic behavior of a reconfigurable hybrid structure. Hinge-connected beam members, stabilized through a secondary system of struts and continuous diagonal cables compose planar n-bar mechanisms arranged in parallel to formulate the spatial reconfigurable structure. The transformability of the system is based on the application of the ‘effective 4-bar’ concept using a sequence of 1-DOF motion steps through selectively locking (n−4) joints of the primary members and modification of the cables’ length. Different intermediate configurations depend on the motion planning, in order to adjust the system’s joints to the desired values during the motion steps involved in the respective transformation sequence. The proposed control system includes position sensors installed on the individual joints to provide feedback information, two motion actuators located at the structural supports, as well as brakes installed on each individual joint. The control system manages the operation of the motion actuators and the brakes to realize the reconfiguration sequences through tensioning the cables. The paper reports the structure’s design concept, motion planning and control. The implementation of the structural reconfiguration approach and related kinematics issues are investigated through a simulation example.

Tuberculosis Biomarker Extraction and Isothermal Amplification in an Integrated Diagnostic Device.

In this study, we integrated magnetic bead-based sample preparation and isothermal loop mediated amplification (LAMP) of TB in a single tube. Surrogate sputum samples produced by the Program for Appropriate Technology in Health containing inactivated TB bacteria were used to test the diagnostic. In order to test the sample preparation method, samples were lysed, and DNA was manually extracted and eluted into water in the tube. In a thermal cycler, LAMP amplified TB DNA from 103 TB cells/mL of sputum at 53.5 ± 3.3 minutes, 104 cells/mL at 46.3 ± 2.2 minutes, and 105 cells/mL at 41.6 ± 1.9 minutes. Negative control samples did not amplify. Next, sample preparation was combined with in-tubing isothermal LAMP amplification by replacing the water elution chamber with a LAMP reaction chamber. In this intermediate configuration, LAMP amplified 103 cells/mL at 74 ± 10 minutes, 104 cells/mL at 60 ± 9 minutes, and 105 TB cells/mL of sputum at 54 ± 9 minutes. Two of three negative controls did not amplify; one amplified at 100 minutes. In the semi-automated system, DNA was eluted directly into an isothermal reaction solution containing the faster OptiGene DNA polymerase. The low surrogate sputum concentration, 103 TB cells/mL, amplified at 52.8 ± 3.3 minutes, 104 cells/mL at 45.4 ± 11.3 minutes, and 105 cells/mL at 31.8 ± 2.9 minutes. TB negative samples amplified at 66.4 ± 7.4 minutes. This study demonstrated the feasibility of a single tube design for integrating sample preparation and isothermal amplification, which with further development could be useful for point-of-care applications, particularly in a low-resource setting.

A new thermodynamical framework for finite strain multiplicative elastoplasticity coupled to anisotropic damage

The thermodynamical framework of an elastoplastic model coupled to anisotropic damage is presented in this paper. In the finite strain context, the proposed model is based on the multiplicative decomposition of the strain gradient into elastic and plastic parts. The anisotropic degradation is introduced by means of a second order tensor and another intermediate configuration is introduced by fictitiously removing this degradation from the plastic intermediate configuration. To enhance the physical meaning of the Mandel-like stress measure work conjugated to the inelastic flow stated in this fictitious configuration, i.e. the “effective stress”, a new damage rate tensor is defined with its associated push-forward and pull-back operations. The emphasis in this paper is placed on the description of the interesting properties of the novel definitions of the push-forward and pull-back operations which are discussed through a thermodynamical framework. Furthermore, a specific constitutive model with the plastic and damage flow rules deduced from the restrictions imposed by the second law of thermodynamics is discussed with an application on an asphalt concrete material where the anisotropic evolution of the damage is highlighted.

The role of binding site on the mechanical unfolding mechanism of ubiquitin.

We apply novel atomistic simulations based on potential energy surface exploration to investigate the constant force-induced unfolding of ubiquitin. At the experimentally-studied force clamping level of 100 pN, we find a new unfolding mechanism starting with the detachment between β5 and β3 involving the binding site of ubiquitin, the Ile44 residue. This new unfolding pathway leads to the discovery of new intermediate configurations, which correspond to the end-to-end extensions previously seen experimentally. More importantly, it demonstrates the novel finding that the binding site of ubiquitin can be responsible not only for its biological functions, but also its unfolding dynamics. We also report in contrast to previous single molecule constant force experiments that when the clamping force becomes smaller than about 300 pN, the number of intermediate configurations increases dramatically, where almost all unfolding events at 100 pN involve an intermediate configuration. By directly calculating the life times of the intermediate configurations from the height of the barriers that were crossed on the potential energy surface, we demonstrate that these intermediate states were likely not observed experimentally due to their lifetimes typically being about two orders of magnitude smaller than the experimental temporal resolution.

Nucleation of a three-state spin model on complex networks

We study the metastability and nucleation of the Blume–Capel model on complex networks, in which each node can take one of three possible spin variables {−1,0,1}. We consider the external magnetic field h to be positive, and let the chemical potential λ vary between −h and h in a low temperature, such that the 1 configuration is stable, and −1 configuration and/or 0 configuration are metastable. Combining the heterogeneous mean-field theory with simulations, we show that there exist four regions with distinct nucleation scenarios depending on the values of h and λ: the system undergoes a two-step nucleation process from −1 configuration to 0 configuration and then to 1 configuration (region I); nucleation becomes a one-step process without an intermediate metastable configuration directly from −1 configuration to 1 configuration (region II(1)) or directly from 0 configuration to 1 configuration (region II(2)) depending on the sign of λ; the metastability of the system vanishes and nucleation is thus irrelevant (region III). Furthermore, we show that in the region I nucleation rates for each step intersect that results in the occurrence of a maximum in the total nucleation rate.

Monte Carlo simulations of nematic and chiral nematic shells.

We present a systematic Monte Carlo simulation study of thin nematic and cholesteric shells with planar anchoring using an off-lattice model. The results obtained using the simple model correspond with previously published results for lattice-based systems, with the number, type, and position of defects observed dependent on the shell thickness with four half-strength defects in a tetrahedral arrangement found in very thin shells and a pair of defects in a bipolar (boojum) configuration observed in thicker shells. A third intermediate defect configuration is occasionally observed for intermediate thickness shells, which is stabilized in noncentrosymmetric shells of nonuniform thickness. Chiral nematic (cholesteric) shells are investigated by including a chiral term in the potential. Decreasing the pitch of the chiral nematic leads to a twisted bipolar (chiral boojum) configuration with the director twist increasing from the inner to the outer surface.

The use of Dynamic Environmental Control Systems (DECS) in Cavities of Double Skin Facades for Energy Savings

Dynamic and adaptive façade components have significant potential for energy efficiency goals. However, it is not yet common to see double skin facade (DSF) buildings integrating dynamic component systems to improve their energy savings. Previous studies have repeatedly found DSF buildings to increase their energy consumption during cooling seasons. Potential exists to counteract this problem by developing a kinetic mechanism within the DSF. The Dynamic Environmental Controls System (DECS) was designed and developed to improve their performance. Its application was examined, evaluated via energy modeling simulations, and showed a decrease of the energy demand.DECS has the ability to dynamically change the cavity compartmentation between four types of DSFs: multi-storey, corridor, shaft box, and box window; and twenty-one intermediate configurations. Their performances were examined in DesignBuilder for three climate zones: Los Angeles, New York, and Houston. The focus was each case study's performance for the hottest and coldest day per climate to determine the efficiency of DSFs in extreme weather conditions. The rationale was to locate the boundaries of their performance from perspective of most improvements via DECS. The energy usage of the intermediate configurations was then examined and the dispersion of the results between all types scrutinized. The simulations were made on hourly time steps, and the most efficient configuration per hour was being selected. The aggregation of all formed the DECS pattern for each 24-hour cycle.Two major results were obtained. The application of DECS and analysis of the generated results lead to a decrease of the energy consumption of DSF buildings for the hottest day up to 3.92%, 2.52% and 1.97% per climate and for the coldest day up to 0.55%, 1.90% and 4.00% accordingly. Secondly, the methodology of the research was made less efficient by the lack of a suitable software interface. This issue is addressed.

Generalised multi-impulsive manoeuvres for optimum spacecraft rendezvous in near-circular orbit

This work describes the design of an impulsive manoeuvres' planner meant for onboard autonomous optimum formation flying reconfigurations in near-circular orbit. The whole variation of the relative orbit is stepwise achieved through intermediate configurations, so that passive safety and delta-v consumption minimisation are pursued. The description of the relative motion is accomplished in terms of relative orbital elements and the reconfiguration plan takes into account mean effects due to the Earth oblateness coefficient and differential drag. Manoeuvres consist of sets of triple tangential impulses and a single out-of-plane burn to establish each intermediate configuration. They are scheduled in time intervals compliant with the user-defined permissible time control windows.

Long-Range Protein Vibrations Dependence on Ligand Binding: Rate Promoting Motions

It has been suggested that long-range intramolecular vibrations in enzymes may provide efficient access to intermediate state configurations, enhancing catalytic turnover rates. Recently we have successfully measured these long-range protein vibrations using an anisotropic THz near-field technique to measure protein crystals, called crystal anisotropy terahertz microscopy (CATM). The method isolates these motions from the isotropic librational background, revealing narrow band resonances. Recent measurements on free chicken-egg white lysozyme (CEWL) and tri-N-acetylglucosamine (3NAG) inhibitor bound CEWL reveal dramatic and reproducible changes in the intramolecular vibrational mode spectra with binding. A large resonance at ∼70 cm−1 for free CEWL, is somewhat suppressed with binding, whereas a new resonance is observed at ∼ 40 cm−1, with binding. This dramatic change in the spectra with binding confirms that the observed resonances arise from intramolecular vibrations, and not crystal phonons. Using normal mode analysis, our calculated CATM spectra find a consistent increase in the low frequency signal with binding. While the density of states does not change appreciably with binding, the overall direction of motion shifts for vibrations in the frequency range where there is a large change in the optical signal. The change in the direction of the vibrational motion results in a change in the motion of the charge distribution and therefore, the dipole derivative, leading to the sensitivity to the trajectories in the terahertz optical absorbance. The remaining question is if these specific motions participate in the structural preorganization of the binding site, and thus promote catalytic activity. We will discuss measurements to answer this long standing question. This work was supported by NSF MRI∧2 grant DBI295998.

Solving Algorithm of Initial Guess of Intermediate Configuration in Multi-step Inverse Finite Element Method

Solving Algorithm of Initial Guess of Intermediate Configuration in Multi-step Inverse Finite Element Method

Effects of nano-sized BiFeO3 addition on the properties of high piezoelectric response (1 − x)Bi0.5Na0.5TiO3–xBi0.5K0.5TiO3 ceramics

The role of BiFeO3 addition on the crystal structure, microstructure, and the electrical and electromechanical properties of high-sensitivity Bi0.5Na0.5TiO3–Bi0.5K0.5TiO3 ferroelectric ceramics for compositions at the morphotropic phase boundary (MPB) is investigated. A perovskite solid solution from nano-sized BiFeO3 and Bi0.5Na0.5TiO3–Bi0.5K0.5TiO3 powders is obtained, in which the persistence of a MPB in the ternary system is demonstrated. The structural characterization, along with the electrical properties, indicates the stabilization of intermediate domain configurations, associated with a decrease of the temperature for the development of the ferroelectric long-range order. As a consequence, high phase-change electromechanical response is found for certain small BiFeO3 additions. This result is very promising for the processing of textured ceramics taking advantage of the decomposition behaviour of BiFeO3. Ceramic texturing is demonstrated, a key technology for developing lead-free piezoelectrics that can replace Pb(Zr,Ti)O3.

Analysis of the rotation-vibration-inversion infrared spectrum of the ν10 and ν14 bands of silacyclobutane

Fourier transform spectra of the four-membered heterocycle silacyclobutane (c-C3H8Si)(SCB) were recorded in the infrared region from 500 to 800cm−1 with a resolution of 0.000959cm−1 using synchrotron radiation from the Canadian Light Source. Two fundamental bands observed in this region have been rotationally analyzed. These correspond to motions best described as the in-plane ring deformation mode (ν10) at ∼543cm−1 and the α-CH2 rocking mode (ν14) at ∼737cm−1. Both bands exhibit complex, dense spectral patterns that arise from ring inversion tunnelling of the puckered SCB ring through a planar (C2v) intermediate configuration. Analysis of these patterns revealed rotation-vibration transitions between states of the same inversion symmetry for the ν10 mode as well as rotation-vibration-inversion transitions that connect states of different inversion symmetry. Only rotation-vibration-inversion transitions are observed in the ν14 band due to symmetry as the vibration (A2) is IR forbidden. In total, 12371 infrared transitions were assigned for the ring deformation and α-CH2 rocking bands and combined with those from analysis of the ring puckering (158cm−1) and SiH2 rocking modes (410cm−1) (Chen and van Wijngaarden, 2013). A 10 state fit was performed from the resulting data set containing 20626 rotation-vibration-inversion transitions and provided accurate band centres, ring inversion splittings, rotational and centrifugal distortion constants for the lowest energy states of the dynamic silacyclobutane ring.

Intermediate Stage Build of Sheet Metal in Progressive Die Design

Intermediate stage build of Multi-station progressive die is to get intermediate configuration of every station and blank by unfolding product configuration reversely. It needs complicated hand computation and drawing to design intermediate stage with traditional method. In this paper, NX PDW module is used to finish the work. According to the shape of sheet metal, parts are simply classified into three types, and for different type of sheet metal part, different method to unfold the product configuration is discussed. The process of building intermediate stage with PDW is intuitive, timesaving, and also easy to modify.

Finite-strain formulation and FE implementation of a constitutive model for powder compaction

A finite-strain formulation is developed, implemented and tested for a constitutive model capable of describing the transition from granular to fully dense state during cold forming of ceramic powder. This constitutive model (as well as many others employed for geomaterials) embodies a number of features, such as pressure-sensitive yielding, complex hardening rules and elastoplastic coupling, posing considerable problems in a finite-strain formulation and numerical implementation. A number of strategies are proposed to overcome the related problems, in particular, a neo-Hookean type of modification to the elastic potential and the adoption of the second Piola–Kirchhoff stress referred to the intermediate configuration to describe yielding. An incremental scheme compatible with the formulation for elastoplastic coupling at finite strain is also developed, and the corresponding constitutive update problem is solved by applying a return mapping algorithm.