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Proteins are large biomolecules that regulate all living organisms and consist of one or several chains. The primary structure of a protein chain is a sequence of amino acid residues whose three main atoms (alpha-carbon, nitrogen, and…
We derive structural and binding energy trends for twenty amino acids, their dipeptides, and their interactions with the divalent cations Ca$^{2+}$, Ba$^{2+}$, Sr$^{2+}$, Cd$^{2+}$, Pb$^{2+}$, and Hg$^{2+}$. The underlying data set consists…
Conformational fluctuations are believed to play an important role in the process by which transcription factor proteins locate and bind their target site on the genome of a bacterium. Using a simple model, we show that the binding time can…
Understanding active electrolocation in weakly electric fish remains a challenging issue. In this article we propose a mathematical formulation of this problem, in terms of partial differential equations. This allows us to detail two…
To confer high specificity and affinity in binding, contacts at interfaces between two interacting macromolecules are expected to exhibit pair preferences for types of atoms or residues. Here we quantify these preferences by measuring the…
The outcome of an epidemic is closely related to the network of interactions between the individuals. Likewise, protein functions depend on the 3D arrangement of their residues and on the underlying energetic interaction network. Borrowing…
The fastest possible collective response of a quantum many-body system is related to its excitations at the highest possible energy. In condensed-matter systems, the corresponding timescale is typically set by the Fermi energy. Taking…
Exploring the protein-folding problem has been a long-standing challenge in molecular biology. Protein folding is highly dependent on folding of secondary structures as the way to pave a native folding pathway. Here, we demonstrate that a…
Membrane proteins are crucial in regulating biomembrane shapes and controlling the dynamic changes in membrane morphology during essential cellular processes. These proteins can localize to regions with their preferred curvatures (curvature…
Lipid membranes form the barrier between the inside and outside of cells and many of their subcompartments. As such, they bind to a wide variety of nano- and micrometer sized objects and, in the presence of strong adhesive forces, strongly…
We present a minimal model of plasma membrane heterogeneity that combines criticality with connectivity to cortical cytoskeleton. Our model is motivated by recent observations of micron-sized critical fluctuations in plasma membrane…
We experimentally demonstrate that the bias-field digitized counterdiabatic quantum optimization (BF-DCQO) algorithm, implemented on IonQ's fully connected trapped-ion quantum processors, offers an efficient approach to solving dense…
Force-clamp spectroscopy reveals the unfolding and disulfide bond rupture times of single protein molecules as a function of the stretching force, point mutations and solvent conditions. The statistics of these times reveal whether the…
Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there isn't a first-principle model to explain this different behaviour. We exploit the network properties of protein structures by introducing novel…
We consider a multiple-species mixture of interacting bosons, $N_1$ bosons of mass $m_1$, $N_2$ bosons of mass $m_2$, and $N_3$ bosons of mass $m_3$ in a harmonic trap of frequency $\omega$. The corresponding intraspecies interaction…
Antibodies are Y-shaped proteins that neutralize pathogens and constitute the core of our adaptive immune system. De novo generation of new antibodies that target specific antigens holds the key to accelerating vaccine discovery. However,…
The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we…
Inorganic nanomaterials and particles with enhanced optical, mechanical or magnetic attributes are currently being developed for a wide range of applications. Safety issues have been formulated however concerning their potential cyto- and…
The key finding in the DNA double helix model is the specific pairing or binding between nucleotides A-T and C-G, and the pairing rules are the molecule basis of genetic code. Unfortunately, no such rules have been discovered for proteins.…
The natural vibrational frequencies of biological particles such as viruses and bacteria encode critical information about their mechanical and biological states as they interact with their local environment and undergo structural…