Search for: All records

Biomolecular condensates are important structures in various cellular processes but are challenging to study using traditional experimental techniques. In silico simulations with residue-level coarse-grained models strike a balance between computational efficiency and chemical accuracy. They could offer valuable insights by connecting the emergent properties of these complex systems with molecular sequences. However, existing coarse-grained models often lack easy-to-follow tutorials and are implemented in software that is not optimal for condensate simulations. To address these issues, we introduce OpenABC, a software package that greatly simplifies the setup and execution of coarse-grained condensate simulations with multiple force fields using Python scripting. OpenABC seamlessly integrates with the OpenMM molecular dynamics engine, enabling efficient simulations with performance on a single GPU that rivals the speed achieved by hundreds of CPUs. We also provide tools that convert coarse-grained configurations to all-atom structures for atomistic simulations. We anticipate that OpenABC will significantly facilitate the adoption of in silico simulations by a broader community to investigate the structural and dynamical properties of condensates.

 

This paper presents the Pinch Sensor, an elastic input device to sense the fine motion and pinch force of the index finger and thumb - the two most used digits of human hands for in-hand object manipulation skills. In addition to open and close, the device would allow a user to control a robotic or simulated two-finger hand to reorient an object in three different ways and their combinations. A unique design of elastic sensing provides the users a high degree of perception resolution, as well as the sensation of holding an object with a certain level of stiffness between the index finger and thumb. These characteristics help the users to fine control the pinch force while carrying out manipulation skills. The design features a small size that allows it to be integrated to a handheld controller. Commonly available off-the-shelf components for consumer electronics are used to achieve affordability and reliability. 

Cytochromecoxidase (CcO) is an essential enzyme in mitochondrial and bacterial respiration. It catalyzes the four-electron reduction of molecular oxygen to water and harnesses the chemical energy to translocate four protons across biological membranes. The turnover of the CcO reaction involves an oxidative phase, in which the reduced enzyme (R) is oxidized to the metastable O_Hstate, and a reductive phase, in which O_His reduced back to the R state. During each phase, two protons are translocated across the membrane. However, if O_His allowed to relax to the resting oxidized state (O), a redox equivalent to O_H, its subsequent reduction to R is incapable of driving proton translocation. Here, with resonance Raman spectroscopy and serial femtosecond X-ray crystallography (SFX), we show that the hemea₃iron and Cu_Bin the active site of the O state, like those in the O_Hstate, are coordinated by a hydroxide ion and a water molecule, respectively. However, Y244, critical for the oxygen reduction chemistry, is in the neutral protonated form, which distinguishes O from O_H, where Y244 is in the deprotonated tyrosinate form. These structural characteristics of O provide insights into the proton translocation mechanism of CcO.