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Water molecules play important roles in all biochemical processes. Therefore, it is of key importance to obtain information of the structure, dynamics, and thermodynamics of water molecules around proteins. Numerous computational methods have been suggested with this aim. In this study, we compare the performance of conventional and grand-canonical Monte Carlo (GCMC) molecular dynamics (MD) simula
The streaming instability is a promising mechanism to induce the formation of planetesimals. Nonetheless, this process has been found in previous studies to require either a dust-to-gas surface density ratio or a dust size that is enhanced compared to observed values. Employing two-dimensional global simulations of protoplanetary disks, we show that the vertical shear instability and the streaming
The increasing carbon dioxide (CO2) concentration in the atmosphere in combination with climatic changes throughout the lastcentury are likely to have had a profound effect on the physiology of trees: altering the carbon andwater fluxes passing throughthe stomatal pores. However, the magnitude and spatial patterns of such changes in natural forests remain highly uncertain.Here, stable carbon isoto
We present an online system for real time recognition of actions involving objects working in online mode. The system merges two streams of information pro- cessing running in parallel. One is carried out by a hierarchical self-organizing map (SOM) system that recognizes the performed actions by analysing the spa- tial trajectories of the agent’s movements. It consists of two layers of SOMs and a
We developed an analytical theory for the many-body potential of mean force (POMF) between N spheres immersed in a continuum chain fluid. The theory is almost exact for a T polymer solution in the protein limit (small particles, long polymers), where N-body effects are important. Polydispersity in polymer length according to a SchulzFlory distribution emerges naturally from our analysis, as does t
Monte Carlo simulations show that charge-regulation alone can cause highly charged zirconium nanoparticles to adsorb to a similarly charged or neutral silica particle and thereby stabilizing the latter. This mechanism, referred to as halo stabilization, is quite general and applicable in a range of systems provided that pH, van der Waals forces, and dissociation constants of the charge-regulating
We use a continuum chain model and develop an analytical theory for the interaction between many spheres immersed in a fluid of ideal polydisperse polymers. Assuming local spherical symmetry of the polymer field about each particle, combined with a local approximation, compact expressions are derived for the many-body interaction between the spheres. We use a mean-field approximation to investigat
The microstructure evolution during cold rolling of commercial purity AA1050 aluminum is investigated through numerical simulations. A finite strain elasto-viscoplastic constitutive model is employed, where the dislocation density and average grain size are taken as variables characterizing the deformed microstructure. Grain size evolution due to dynamic recrystallization is considered and the mic
The pair interaction between two charged colloidal particles, in the presence of a polyelectrolyte as well as simple salt, is analyzed theoretically. Of particular interest is the way in which such a combination of salts can be used to induce a strong, long-range attraction, with at most a minor free energy barrier. We show that the nature of the simple salt is highly relevant, i.e., 2:1, 1:1, and
A direct numerical simulation (DNS) coupling with multi-zone chemistry mapping (MZCM) is presented to simulate flame propagation and auto-ignition in premixed fuel/air mixtures. In the MZCM approach, the physical domain is mapped into a low-dimensional phase domain with a few thermodynamic variables as the independent variables. The approach is based on the fractional step method, in which the flo
This study explores the concept of pasture, looking at how people classify it and the features that determine how an image is classified. The analysis is based on two parallel studies that used the same image material. The first study was a web-based survey in which respondents were asked to make a pairwise comparison of the images they felt best corresponded to pasture. The second study used eye-
Understanding the driving forces governing protein assembly requires the characterization of interactions at molecular level. We focus on two homologous oppositely charged proteins, lysozyme and alpha-lactalbumin, which can assemble into microspheres. The assembly early steps were characterized through the identification of interacting surfaces monitored at residue level by NMR chemical shift pert
This work deals with inverse-motion-based form finding for electroelasticity. The inverse motion problem is formulated for the electroelastic case, and the resulting equations are implemented within a finite element framework. A four-field variational approach is adopted, taking into consideration the typically incompressible behavior of the elastomer materials commonly used in electromechanical a
A fully divergence-free method is proposed for generation of inhomogeneous/anisotropic turbulence with large spatial variation. The method is based on the method of Smirnov et al., which is known to violate the divergence-free constraint when spatial variation of turbulence is present. In the proposed method a vector potential field is introduced; by taking the vector curl of the potential field o
Effective pair potentials between charged colloids, obtained from Monte Carlo simulations of two single colloids in a closed cell at the primitive model level, are shown to reproduce accurately the structure of aqueous salt-free colloidal dispersions, as determined from full primitive model simulations by Linse et al. (Linse, P.; Lobaskin, V. Electrostatic Attraction and Phase Separation in Soluti
