Comprehensive Fitness Landscape of a Multi-Geometry Protein Capsid Informs Machine Learning Models of Assembly

Virus-like particles (VLPs) are non-infections viral-derived nanomaterials poised for biotechnological applications due to their well-defined, modular self-assembling architecture. Although progress has been made in understanding the complex effects that mutations may have on VLPs, nuanced understanding of the influence particle mutability has on quaternary structure has yet to be achieved. Here, we generate and compare the apparent fitness landscapes of two capsid geometries (T=3 and T=1 icosahedral) of the bacteriophage MS2 VLP. We find significant shifts in mutability at the symmetry interfaces of the T=1 capsid when compared to the wildtype T=3 assembly. Furthermore, we use the generated landscapes to benchmark the performance of in silico mutational scanning tools in capturing the effect of missense mutation on complex particle assembly. Finding that predicted stability effects correlated relatively poorly with assembly phenotype, we used a combination of de novo features in tandem with in silico results to train machine learning algorithms for the classification of variant effects on assembly. Our findings not only reveal ways that assembly geometry affects the mutable landscape of a self-assembled particle, but also establish a template for the generation of predictive mutational models of self-assembled capsids using minimal empirical training data.

Flocculation in Estuaries: Modeling, Laboratory and In-situ Studies

Modelling the flocculation of particles in a natural environment like an estuary is a challenging task owing to the complex particle-particle and particle-hydrodynamic interactions involved. In this chapter a summary is given of recent laboratory and in-situ studies regarding flocculation. A flocculation model is presented and the way to implement it in an existing sediment transport model is discussed. The model ought to be parametrized, which can be done by performing laboratory experiments which are reviewed. It is found, both from laboratory and in-situ studies, that flocculation between mineral sediment and organic matter is the dominant form of flocculation in estuarine systems. Mineral sediment in the water column is < 20 μm in size and its settling velocity is in the range [0–0.5] mm/s. Flocs can then be categorized in two types: flocs of size [20–200] μm and flocs of size > 200 μm. The origin of these two types is discussed. The two types of flocs are found at different positions in the water column and both have settling velocities in the range [0.5–10] mm/s.

Acoustic tweezer with complex boundary-free trapping and transport channel controlled by shadow waveguides

Acoustic tweezers use ultrasound for contact-free, bio-compatible, and precise manipulation of particles from millimeter to submicrometer scale. In microfluidics, acoustic tweezers typically use an array of sources to create standing wave patterns that can trap and move objects in ways constrained by the limited complexity of the acoustic wave field. Here, we demonstrate spatially complex particle trapping and manipulation inside a boundary-free chamber using a single pair of sources and an engineered structure outside the chamber that we call a shadow waveguide. The shadow waveguide creates a tightly confined, spatially complex acoustic field inside the chamber without requiring any interior structure that would interfere with net flow or transport. Altering the input signals to the two sources creates trapped particle motion along an arbitrary path defined by the shadow waveguide. Particle trapping, particle manipulation and transport, and Thouless pumping are experimentally demonstrated.

Implementation and Impact of Virtual Reality on Survival Horror Games

Currently, games are an important part of human life. Not only serves as entertainment, games nowadays also serve as education, communication, socialization, and even a job for some people. This makes technology in the game world more developed and closer to reality. One of the popular and interesting technologies is virtual reality. This technology has various elements, but the most important element is the immersion element, which can give users the sensation to feel as if they are in a real environment. In this research, the authors examine the effects of virtual reality when combined with horror games. The selection of horror games was made because this genre is one of the genres with the fastest immersion element compared to other game genres. In addition to the use of virtual reality technology, considering that horror games require complex particle simulations and good lighting, the authors use the Unreal Engine as the main engine in this game. The test method used in this study is the beta testing method with the assessment using the user acceptance method. The conclusion was that virtual reality technology combined with the advantages of the unreal engine caused game players to get a tenser atmosphere.

Enrichment a Study of Structural, Optical and Dielectric Properties of Mowiol 4-88 (Pva) Filled Zno Nanocomposites

The use of ZnO nanoparticles in the fabrication of PVA (Mowiol 4-88) nanocomposites with different ‘x’ filling compositions through solvent casting technique leading to the enrichment of the host's physical properties is presented. The sol-gel approach synthesizes Zinc Oxide (ZnO) nanoparticles. The formation of ZnO nanoparticles of size 100 nm was confirmed through X-ray powder diffraction (XRD) and Field Effect Scanning Electron Microscope (FESEM) techniques. The XRD technique determines the appearance of nanocomposites and their structural properties. The improvement in filling concentration enhances the particle size up to 150 nm and percentage crystallinity by 41 % for optimum filler composition. The FTIR spectra demonstrate ZnO nanofillers' binding with OH group of host Mowiol 4-88 through intra or inter hydrogen bonding leading to a complex conformation. The optical studies indicate a decrease in the energy gap with the rise in filler composition up to 15 wt%, and frequency-dependent dielectric constant characterization shows the enhancement in the dielectric constant with an optimum filling concentration 15 wt% ZnO nanofillers. FESEM image confirms homogenous distribution and complex particle size of incorporated ZnO nanoparticles in the PVA matrix. HIGHLIGHTS ZnO nanoparticles with Fabrication of PVA (Mowiol 4-88) nanocomposites through solvent casting technique ZnO nanoparticles of size 100 nm was confirmed Filling concentration enhances the particle size and percentage crystallinity SEM and EDS illustrate ZnO nanofiller’s systematic distribution Dielectric measurements show that these fabricated polymeric composites are polar GRAPHICAL ABSTRACT

TSSC4 is a component of U5 snRNP that promotes tri-snRNP formation

U5 snRNP is a complex particle essential for RNA splicing. U5 snRNPs undergo intricate biogenesis that ensures that only a fully mature particle assembles into a splicing competent U4/U6•U5 tri-snRNP and enters the splicing reaction. During splicing, U5 snRNP is substantially rearranged and leaves as a U5/PRPF19 post-splicing particle, which requires re-generation before the next round of splicing. Here, we show that a previously uncharacterized protein TSSC4 is a component of U5 snRNP that promotes tri-snRNP formation. We provide evidence that TSSC4 associates with U5 snRNP chaperones, U5 snRNP and the U5/PRPF19 particle. Specifically, TSSC4 interacts with U5-specific proteins PRPF8, EFTUD2 and SNRNP200. We also identified TSSC4 domains critical for the interaction with U5 snRNP and the PRPF19 complex, as well as for TSSC4 function in tri-snRNP assembly. TSSC4 emerges as a specific chaperone that acts in U5 snRNP de novo biogenesis as well as post-splicing recycling.

Simulations Of Steady Flows Through Cylindrical Geometries With And Without Local Constrictions By Multiparticle Collision Dynamics

In this thesis, a recently developed particle-based method called multiparticle collision dynamics (MPC) is used to simulate steady flows through three-dimensional constricted axisymmetric cylinders. The work is motivated by complex particle interactions in blood flow such as aggregation and the need to be able to capture these effects in physiologically relevant complex flow geometries. This is the first time that MPC dynamics has been applied to simulate flows though constrictions. The particle collisions in MPC dynamics are numerically more efficient than other particle-based simulation methods. Particle interactions with the cylinder walls are modeled using bounce-back (BB) and loss in tangential, reversal of normal (LIT) boundary conditions. BB is an analog of the macroscopic no-slip boundary condition, and LIT gives slip. Finally, an averaging procedure is employed to make a connection with the solution to the Navier-Stokes equations. Interesting differences have been found in the velocity profiles obtained using MPC with BB and LIT, compared to Navier-Stokes.

Simulations Of Steady Flows Through Cylindrical Geometries With And Without Local Constrictions By Multiparticle Collision Dynamics

In this thesis, a recently developed particle-based method called multiparticle collision dynamics (MPC) is used to simulate steady flows through three-dimensional constricted axisymmetric cylinders. The work is motivated by complex particle interactions in blood flow such as aggregation and the need to be able to capture these effects in physiologically relevant complex flow geometries. This is the first time that MPC dynamics has been applied to simulate flows though constrictions. The particle collisions in MPC dynamics are numerically more efficient than other particle-based simulation methods. Particle interactions with the cylinder walls are modeled using bounce-back (BB) and loss in tangential, reversal of normal (LIT) boundary conditions. BB is an analog of the macroscopic no-slip boundary condition, and LIT gives slip. Finally, an averaging procedure is employed to make a connection with the solution to the Navier-Stokes equations. Interesting differences have been found in the velocity profiles obtained using MPC with BB and LIT, compared to Navier-Stokes.

Soft Sensor Development for Real-Time Process Monitoring of Multidimensional Fractionation in Tubular Centrifuges

High centrifugal acceleration and throughput rates of tubular centrifuges enable the solid–liquid size separation and fractionation of nanoparticles on a bench scale. Nowadays, advantageous product properties are defined by precise specifications regarding particle size and material composition. Hence, there is a demand for innovative and efficient downstream processing of complex particle suspensions. With this type of centrifuge working in a semi-continuous mode, an online observation of the separation quality is needed for optimization purposes. To analyze the composition of fines downstream of the centrifuge, a UV/vis soft sensor is developed to monitor the sorting of polymer and metal oxide nanoparticles by their size and density. By spectroscopic multi-component analysis, a measured UV/vis signal is translated into a model based prediction of the relative solids volume fraction of the fines. High signal stability and an adaptive but mandatory calibration routine enable the presented setup to accurately predict the product’s composition at variable operating conditions. It is outlined how this software-based UV/vis sensor can be utilized effectively for challenging real-time process analytics in multi-component suspension processing. The setup provides insight into the underlying process dynamics and assists in optimizing the outcome of separation tasks on the nanoscale.

Isotopically Light Cd in Sediments Underlying Oxygen Deficient Zones

Cadmium is a trace metal of interest in the ocean partly because its concentration mimics that of phosphate. However, deviations from the global mean dissolved Cd/PO4 relationship are present in oxygen deficient zones, where Cd is depleted relative to phosphate. This decoupling has been suggested to result from cadmium sulphide (CdS) precipitation in reducing microenvironments within sinking organic matter. We present Cd concentrations and Cd isotope compositions in organic-rich sediments deposited at several upwelling sites along the northeast Pacific continental margin. These sediments all have enriched Cd concentrations relative to crustal material. We calculate a net accumulation rate of Cd in margin settings of between 2.6 to 12.0 × 107 mol/yr, higher than previous estimates, but at the low end of a recently published estimate for the magnitude of the marine sink due to water column CdS precipitation. Cadmium in organic-rich sediments is isotopically light (δ114/110CdNIST-3108 = +0.02 ± 0.14‰, n = 26; 2 SD) compared to deep seawater (+0.3 ± 0.1‰). However, isotope fractionation during diagenesis in continental margin settings appears to be small. Therefore, the light Cd isotope composition of organic-rich sediments is likely to reflect an isotopically light source of Cd. Non-quantitative biological uptake of light Cd by phytoplankton is one possible means of supplying light Cd to the sediment, which would imply that Cd isotopes could be used as a tracer of past ocean productivity. However, water column CdS precipitation is also predicted to preferentially sequester light Cd isotopes from the water column, which could obfuscate Cd as a tracer. We also observe notably light Cd isotope compositions associated with elevated solid phase Fe concentrations, suggesting that scavenging of Cd by Fe oxide phases may contribute to the light Cd isotope composition of sediments. These multiple possible sources of isotopically light Cd to sediments, along with evidence for complex particle cycling of Cd in the water column, bring into question the straightforward application of Cd isotopes as a paleoproductivity proxy.