Development of the AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Simulation) force field for proteins is presented. The current version (AMOEBA-2013) utilizes permanent electrostatic multipole moments through the quadrupole at each atom, and explicitly treats polarization effects in various chemical and physical environments. The atomic multipole electrostatic parameters for ea...

Stenotrophomonas maltophilia is found ubiquitously in the environment and is an important emerging nosocomial pathogen. S. maltophilia has been recently described as an Amoebae-Resistant Bacteria (ARB) that exists as part of the microbiome of various free-living amoebae (FLA) from waters. Co-culture approaches with Vermamoeba vermiformis demonstrated the ability of this bacterium to resist amoe...

The social amoeba Dictyostelium discoideum has proven to be a useful model for studying relevant aspects of the host-pathogen interaction. In this work, D. discoideum was used as a model to study the ability of Salmonella Typhimurium to survive in amoebae and to evaluate the contribution of selected genes in this process. To do this, we performed infection assays using axenic cultures of D. dis...

While a considerable body of information on the synthesis and localization of ribonucleic acid (RNA) in Amoeba proteus has been accumulated in recent years, very little is known about desoxy-ribonucleic acid (DNA) in this organism. In the course of numerous autoradiographic experiments with p32, C14_adenine, and C14-orotic acid (1) RNA was found to be the only demonstrably labelled, acid-insolu...

Assessment of chemical properties can often require a computationally costly sampling of a high-dimensional phase space in order accurately to predict ensemble-averaged values. Molecular mechanics simulations offer an efficient way to sample such ensembles, with the quality of the results depending on the ability of the force field adequately to describe the energetics of the system under the c...

We prove that if Q is a nw-nep forcing then it cannot add a dominating real. We also show that amoeba forcing cannot be P(X)/I if I is an א1-complete ideal. Furthermore, we generalize the results of [Sh 480]. I would like to thank Alice Leonhardt for the beautiful typing. This research was partially supported by the Israel Science Foundation founded by the Israel Academy of Sciences and Humanit...

We study compactifications of very affine varieties defined by imposing a polyhedral structure on the non-archimedean amoeba. These com-pactifications have divisorial boundary with combinatorial normal croosings. We consider some examples including M 0,n ⊂ M 0,n (and more generally log canonical models of complements of hyperplane arrangements) and tropical recompactifications of Chow quotients...