The effects of asymmetry in active noises on the efficiency of single colloidal Stirling engines with active noises.

Molecular machines, which operate in highly fluctuating environments far from equilibrium, may benefit from their non-equilibrium environments. It is, however, a topic of controversy how the efficiency of the microscopic engines can be enhanced. Recent experiments showed that microscopic Stirling engines in bacterial reservoirs could show high performance beyond the equilibrium thermodynamics. In this work, we perform overdamped Langevin dynamics simulations for microscopic Stirling heat engines in bacterial reservoirs and show that the temperature dependence of the magnitude of active noises should be responsible for such high efficiency. Only when we introduce temperature-dependent active noises, the efficiency of the microscopic Stirling engines is enhanced significantly as in experiments.

Panoramic dental tomosynthesis imaging by use of CBCT projection data.

Dental CBCT and panoramic images are important imaging modalities used in dental diagnosis and treatment planning. In order to acquire a panoramic image without an additional panoramic scan, in this study, we proposed a method of reconstructing a panoramic image by extracting panoramic projection data from dental CBCT projection data. After specifying the patient's dental arch from the patient's CBCT image, panoramic projection data are extracted from the CBCT projection data along the appropriate panoramic scan trajectory that fits the dental arch. A total of 40 clinical human datasets and one head phantom dataset were used to test the proposed method. The clinical human dataset used in this study includes cases in which it is difficult to reconstruct panoramic images from CBCT images, such as data with severe metal artifacts or data without teeth. As a result of applying the panoramic image reconstruction method proposed in this study, we were able to successfully acquire panoramic images from the CBCT projection data of various patients. The proposed method acquires a universally applicable panoramic image that is less affected by CBCT image quality and metal artifacts by extracting panoramic projection data from dental CBCT data and reconstructing a panoramic image.

Dynamics of equilibrium-linked colloidal networks.

Colloids that attractively bond to only a few neighbors (e.g., patchy particles) can form equilibrium gels with distinctive dynamic properties that are stable in time. Here, we use a coarse-grained model to explore the dynamics of linked networks of patchy colloids whose average valence is macroscopically, rather than microscopically, constrained. Simulation results for the model show dynamic hallmarks of equilibrium gel formation and establish that the colloid-colloid bond persistence time controls the characteristic slow relaxation of the self-intermediate scattering function. The model features re-entrant network formation without phase separation as a function of linker concentration, centered at the stoichiometric ratio of linker ends to nanoparticle surface bonding sites. Departures from stoichiometry result in linker-starved or linker-saturated networks with reduced connectivity and shorter characteristic relaxation times with lower activation energies. Underlying the re-entrant trends, dynamic properties vary monotonically with the number of effective network bonds per colloid, a quantity that can be predicted using Wertheim's thermodynamic perturbation theory. These behaviors suggest macroscopic in situ strategies for tuning the dynamic response of colloidal networks.

Temperature Dependence of Conformational Relaxation of Poly(ethylene oxide) Melts.

The time-temperature superposition (TTS) principle, employed extensively for the analysis of polymer dynamics, is based on the assumption that the different normal modes of polymer chains would experience identical temperature dependence. We aim to test the critical assumption for TTS principle by investigating poly(ethylene oxide) (PEO) melts, which have been considered excellent solid polyelectrolytes. In this work, we perform all-atom molecular dynamics simulations up to 300 ns at a range of temperatures for PEO melts. We find from our simulations that the conformations of strands of PEO chains in melts show ideal chain statistics when the strand consists of at least 10 monomers. At the temperature range of T= 400 to 300 K, the mean-square displacements (⟨Δr2(t)⟩) of the centers of mass of chains enter the Fickian regime, i.e., ⟨Δr2(t)⟩∼t1. On the other hand, ⟨Δr2(t)⟩ of the monomers of the chains scales as ⟨Δr2(t)⟩∼t1/2 at intermediate time scales as expected for the Rouse model. We investigate various relaxation modes of the polymer chains and their relaxation times (τn), by calculating for each strand of n monomers. Interestingly, different normal modes of the PEO chains experience identical temperature dependence, thus indicating that the TTS principle would hold for the given temperature range.

Confinement effects on the mechanical heterogeneity of polymer fiber glasses.

Both polymer fiber glasses and bulk polymer glasses exhibit nonlinear mechanical responses under uniaxial deformation. In polymer fibers, however, polymer chains are confined strongly and the surface area is relatively large compared to their volume. The confinement and the surface may lead to the spatially heterogeneous relaxation of chains in polymer fibers. In this work we perform molecular dynamics simulations and investigate the relation between the heterogeneous dynamics and the nonlinear mechanical responses at a molecular level. Our molecular simulations capture successfully not only the nonlinear mechanical response but also the dependence of mechanical properties on the strain rate of typical polymer glasses as in experiments. We find that the local elastic modulus and the nonaffine displacement are spatially heterogeneous in the pre-yield regime, which results in a lower elastic modulus for polymer fibers than bulk polymer glasses. In the post-yield regime, those mechanical properties become relatively homogeneous. Monomers with large nonaffine displacement are localized mainly at the interfacial region in the pre-yield regime while highly nonaffine monomers are distributed throughout the fibers in the post-yield regime. We show that the nonaffine displacement during deformation relates closely to the mechanical response of the polymer fibers. We also find that in the strain-hardening regime there is a significant difference in the energetic contribution to the stress between polymer fibers and bulk polymers, for which the modulus of the strain-hardening regime of the polymer fibers is smaller than that of bulk polymers.

Enhancement of soft-tissue contrast in cone-beam CT using an anti-scatter grid with a sparse sampling approach.

PURPOSE: Anti-scatter grids suppress the scatter substantially thus improving image contrast in radiography. However, its active use in cone-beam CT for the purpose of improving contrast-to-noise ratio (CNR) has not been successful mainly due to the increased noise related to Poisson statistics of photons. This paper proposes a sparse-view scanning approach to address the above issue. METHOD: Compared to the conventional cone-beam CT imaging framework, the proposed method reduces the number of projections and increases exposure in each projection to enhance image quality without an additional cost of radiation dose to patients. For image reconstruction from sparse-view data, an adaptive-steepest-descent projection-onto-convex-sets (ASD POCS) algorithm regularized by total-variation (TV) minimization was adopted. Contrast and CNR with various scattering conditions were evaluated in projection domain by a simulation study using GATE. Then we evaluated contrast, resolution, and image uniformity in CT image domain with Catphan phantom. A head phantom with soft-tissue structures was also employed for demonstrating a realistic application. A virtual grid-based estimation and reduction of scatter has also been implemented for comparison with the real anti-scatter grid. RESULTS: In the projection domain evaluation, contrast and CNR enhancement was observed when using an anti-scatter grid compared to the virtual grid. In the CT image domain, the proposed method produced substantially higher contrast and CNR of the low-contrast structures with much improved image uniformity. CONCLUSION: We have shown that the proposed method can provide high-quality CBCT images particularly with an increased contrast of soft-tissue at a neutral dose for image-guidance.

Stochastic and Heterogeneous Cancer Cell Migration: Experiment and Theory.

Cell migration, an essential process for normal cell development and cancer metastasis, differs from a simple random walk: the mean-square displacement (〈(Δr)2(t)〉) of cells sometimes shows non-Fickian behavior, and the spatiotemporal correlation function (G(r, t)) of cells is often non-Gaussian. We find that this intriguing cell migration should be attributed to heterogeneity in a cell population, even one with a homogeneous genetic background. There are two limiting types of heterogeneity in a cell population: cellular heterogeneity and temporal heterogeneity. Cellular heterogeneity accounts for the cell-to-cell variation in migration capacity, while temporal heterogeneity arises from the temporal noise in the migration capacity of single cells. We illustrate that both cellular and temporal heterogeneity need to be taken into account simultaneously to elucidate cell migration. We investigate the two-dimensional migration of A549 lung cancer cells using time-lapse microscopy and find that the migration of A549 cells is Fickian but has a non-Gaussian spatiotemporal correlation. We find that when a theoretical model considers both cellular and temporal heterogeneity, the model reproduces all of the anomalous behaviors of cancer cell migration.

Spatial Dependence of Non-Gaussian Diffusion of Nanoparticles in Free-Standing Thin Polymer Films.

The addition of nanoparticles (NPs) to a free-standing polymer film affects the properties of the film such as viscosity and glass transition temperature. Recent experiments, for example, showed that the glass transition temperature of thin polymer films was dependent on how NPs were distributed within the polymer films. However, the spatial arrangement of NPs in free-standing polymer films and its effect on the diffusion of NPs and polymers remain elusive at a molecular level. In this study, we employ generic coarse-grained models for polymers and NPs and perform extensive molecular dynamics simulations to investigate the diffusion of polymers and NPs in free-standing thin polymer films. We find that small NPs are likely to stay at the interfacial region of the polymer film, while large NPs tend to stay at the center of the film. On the other hand, as the interaction between a NP and a monomer becomes more attractive, the NP is more likely to be placed at the film center. The diffusion of monomers slows down slightly as more NPs are added to the film. Interestingly, the NP diffusion is dependent strongly on the spatial arrangement of the NPs: NPs at the interfacial region diffuse faster and undergo more non-Gaussian diffusion than NPs at the film center, which implies that the interfacial region would be more mobile and dynamically heterogeneous than the film center. We also find that the mechanism for non-Gaussian diffusion of NPs at the film center differs from that at the interfacial region and that the NP diffusion would reflect the local viscosity of the polymer films.

A Theoretical Model for the Cell Cycle and Drug Induced Cell Cycle Arrest of FUCCI Systems with Cell-to-Cell Variation during Mitosis.

PURPOSE: Since the molecular mechanism of the cell cycle was established, various theoretical models of this process have been developed. A recent study revealed significant variability in cell cycle duration between mother and daughter cells, but this observation has not been incorporated into the theoretical models. METHODS: We used fluorescent ubiquitination-based cell cycle indicator (FUCCI) systems and live-monitored the heterogeneity of cell cycle progression within daughter cells, which accounts for dephasing synchrony. To incorporate the variable cell cycle durations into a model, we modified a two-ordinary differential equation (ODE) model based on reciprocal activation between CDK1 and APC. RESULTS: Our model reproduced the experimental population profile, in which cell cycle synchrony dephased due to variability. Based on this model, we determined parameters for CDK1 and APC in the cell cycle profile after treatment with antimitotic drugs and associated the parameters with the drugs' mode of action as cell cycle inhibitors. CONCLUSION: This suggests that this model is useful for determining the mode of action of unknown small molecules on the cell cycle.

Effect of methane-sugar interaction on the solubility of methane in an aqueous solution.

In this study, the effect of methane-sugar interaction on the solubility of methane in an aqueous solution at ambient pressure was investigated. Various sugars, such as fructose, glucose, sucrose, maltose, and raffinose, were used, and depending on the type and concentration of sugar, the methane solubility increased from 21.72mg/L (in pure water) to 24.86mg/L. Sugars with a low hydrogen-bonding number between the water and sugar molecules exhibited a large enhancement in methane solubility. The solute partitioning model and molecular dynamics simulations were employed to verify the results obtained for the experimental solubility of methane in aqueous sugar solutions.