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Atomic motions and energetics for a phosphate transfer reaction catalyzed by the cAMP-dependent protein kinase (PKA) are calculated by plane-wave density functional theory, starting from structures of proteins crystallized in both the…
We examine driven superconducting vortices interacting with quenched disorder where we measure the memory effects under a sequence of drive pulses applied perpendicular to each other. As a function of disorder strength, we find four types…
We investigate the melting behavior of calcium oxide (CaO) under extreme conditions, a problem that remains poorly constrained due to experimental limitations despite its relevance for geophysical and technological applications. We develop…
The functionalities of a wide range of optical and opto-electronic devices are based on resonance effects and active tuning of the amplitude and wavelength response is often essential. Plasmonic nanostructures are an efficient way to create…
Structural flexibility and/or dynamic interactions with other molecules is a critical aspect of protein function. CryoEM provides direct visualization of individual macromolecules sampling different conformational and compositional states.…
Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. Simple models defined by contact topology, known as elastic network models, have been used to model a variety of systems, but the…
Recent work suggests that large-scale, multi-animal modeling can significantly improve neural recording analysis. However, for functional calcium traces, existing approaches remain task-specific, limiting transfer across common neuroscience…
Understanding charge storage in low-dimensional electrodes is crucial for developing novel ecologically friendly devices for capacitive energy storage and conversion, water desalination, etc. Exactly-solvable models allow in-depth analyses…
The effect of mutations on protein structures is usually rather localized and minor. Finding a mutation that can single-handedly change the fold and/or topology of a protein structure is a rare exception. The A31P mutant of the homodimeric…
The Fenna Mathews Olson (FMO) complex of green sulphur bacteria is an example of a photosynthetic pigment protein complex, in which the electronic properties of the pigments are modified by the protein environment to promote efficient…
The $\alpha$ and $\beta$ subunits comprising the hexameric assembly of F1-ATPase share a high degree of structural identity, though low primary identity. Each subunit binds nucleotide in similar pockets, yet only $\beta$ subunits are…
Protein structure prediction often hinges on multiple sequence alignments (MSAs), which underperform on low-homology and orphan proteins. We introduce PLAME, a lightweight MSA design framework that leverages evolutionary embeddings from…
Intracellular calcium is regulated in part by the release of Ca$^{2+}$ ions from the endoplasmic reticulum via inositol-4,5-triphosphate receptor (IP$_3$R) channels (among other possibilities such as RyR and L-type calcium channels). The…
Phase changing materials (PCM) are widely used for optical data recording, sensing, all-optical switching, and optical limiting. Our focus here is on the case when the change in the transmission characteristics of the optical material is…
Biological systems achieve adaptive mechanical responses through reaction-diffusion processes that couple chemical wave propagation to structural transitions. Although synthetic hydrogels with enzymatic reactions offer a platform for…
Unicellular organisms are open metabolic systems that need to process information about their external environment in order to survive. In most types of tissues and organisms, cells use calcium signaling to carry information from the…
Observations of single epidermal cells on flat adhesive substrates have revealed two distinct morphological and functional states, namely a non-migrating symmetric unpolarized state and a migrating asymmetric polarized state. These states…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
Partial substitution of the clinker in the cement by a supplementary cementitious material (SCM) is one of the main solutions to reduce the carbon footprint. Calcined kaolinite is a good candidate due to its availability and relatively high…
Recently, a new concept for continuum robots capable of producing macro-scale and micro-scale motion has been presented. These robots achieve their multi-scale motion capabilities by coupling direct-actuation of push-pull back-bones for…