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Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in…
Although ligand-binding sites in many proteins contain a high number density of charged side chains that can polarize small organic molecules and influence binding, the magnitude of this effect has not been studied in many systems. Here, we…
Designing protein-binding proteins with high affinity is critical in biomedical research and biotechnology. Despite recent advancements targeting specific proteins, the ability to create high-affinity binders for arbitrary protein targets…
Domain-wall dynamics in ferroelectric materials are strongly position-dependent since each polar interface is locked into a unique local microstructure. This necessitates spatially resolved studies of the wall-pinning using scanning-probe…
We show clear experimental evidence of co-operative terahertz (THz) dynamics observed below 3 THz (~100 cm-1), for a low-symmetry Zr-based metal-organic framework (MOF) structure, termed MIL-140A [ZrO(O2C-C6H4-CO2)]. Utilizing a combination…
Recognition and binding of specific sites on DNA by proteins is central for many cellular functions such as transcription, replication, and recombination. In the process of recognition, a protein rapidly searches for its specific site on a…
The presence of knots has been observed in a small fraction of single-domain proteins and related to their thermodynamic and kinetic properties. The exchanging of identical structural elements, typical of domain-swapped proteins, make such…
It has been established that Terahertz (THz) band signals can interact with biomolecules through resonant modes. Specifically, of interest here, protein activation. Our research goal is to show how directing the mechanical signaling inside…
We investigate the domain structure of pair contact process with diffusion (PCPD). PCPD is a stochastic reaction-diffusion model which evolves by the competition of two binary reactions, $2A \to 3A$ and $2A \to 0$. In addition, each…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in absence of any…
Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at…
Domains walls and topological defects in ferroelectric materials have emerged as a powerful new paradigm for functional electronic devices including memory and logic. Similarly, wall interactions and dynamics underpin a broad range of…
Neurotransmitter receptor molecules, concentrated in postsynaptic domains along with scaffold and a number of other molecules, are key regulators of signal transmission across synapses. Employing experiment and theory, we develop a…
Cooperativity is a hallmark of proteins, many of which show a modular architecture comprising discrete structural domains. Detecting and describing dynamic couplings between structural regions is difficult in view of the many-body nature of…
Mucin glycoprotein consist of tandem repeating glycosylated regions flanked by non-repetitive protein domains with little glycosylation. These non-repetitive domains are involved in the pH dependent gelation of gastric mucin, which is…
Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To…
Understanding cellular response to mechanical forces is immensely important for a plethora of biological processes. Focal adhesions are multi-molecular protein assemblies that connect the cell to the extracellular matrix and play a pivotal…
Here we reveal details of the interaction between human lysozyme proteins, both native and fibrils, and their water environment by intense terahertz time domain spectroscopy. With the aid of a rigorous dielectric model, we determine the…
The domain size dependence of piezoelectric properties of ferroelectrics is investigated using a continuum Ginzburg-Landau model that incorporates the long-range elastic and electrostatic interactions. Microstructures with desired domain…