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Multilayer assemblies of metal nanoparticles can act as photonic structures, where collective plasmon resonances hybridize with cavity modes to create plasmon-polariton states. For sufficiently strong coupling, plasmon polaritons…
Impact processes of nanoclusters subject to thermal fluctuations are investigated, theoretically. In the former half of the paper, we discuss the basis of quasi-static theory. In the latter part, we carry out the molecular dynamics…
Membrane proteins often need to be inserted into or attached on the cell membrane to perform their functions. Understanding their transmembrane topology and conformational dynamics during insertion is crucial for elucidating their roles.…
Dynamical systems on networks with adaptive couplings appear naturally in real-world systems such as power grid networks, social networks as well as neuronal networks. We investigate a paradigmatic system of adaptively coupled phase…
Protein structure prediction and folding are fundamental to understanding biology, with recent deep learning advances reshaping the field. Diffusion-based generative models have revolutionized protein design, enabling the creation of novel…
Monolayer cluster growth in far-from-equilibrium systems is investigated by applying simulation and analytic techniques to minimal hard core particle (exclusion) models. The first model (I), for post-deposition coarsening dynamics, contains…
Biofilament-motor protein complexes are ubiquitous in biology and drive the transport of cargo vital for many fundamental cellular processes. As they move, motor proteins exert compressive forces on the filaments to which they are attached,…
Nanoindentation, a common technique for probing the mechanical properties of crystalline materials, exhibits both surface and bulk-dominated responses that are linked to the parent crystal's elasticity and plasticity. For FCC crystals, the…
A new model that describes adsorption and clustering of particles on a surface is introduced. A {\it clustering} transition is found which separates between a phase of weakly correlated particle distributions and a phase of strongly…
Protein function is inherently linked to its localization within the cell, and fluorescent microscopy data is an indispensable resource for learning representations of proteins. Despite major developments in molecular representation…
Microtubules and motor proteins are building blocks of self-organized subcellular biological structures such as the mitotic spindle and the centrosomal microtubule array. These same ingredients can form new "bioactive" liquid-crystalline…
Multistationarity in molecular systems underlies switch-like responses in cellular decision making. Determining whether and when a system displays multistationarity is in general a difficult problem. In this work we completely determine the…
An all-atom model of proteins is used to show that the same sequence of amino acids can have many alternative structures, that are very distant from, and that can be as stable as, the corresponding native structure. Such alternative…
Revealing the structure of complex biological macromolecules, such as proteins, is an essential step for understanding the chemical mechanisms that determine the diversity of their functions. Synchrotron based x-ray crystallography and…
Biological diversity has evolved despite the essentially infinite complexity of protein sequence space. We present a hierarchical approach to the efficient searching of this space and quantify the evolutionary potential of our approach with…
Biomolecular folding and function are often coupled. During molecular recognition events, one of the binding partners may transiently or partially unfold, allowing more rapid access to a binding site. We describe a simple model for this…
Protein pattern formation is essential for the spatial organization of many intracellular processes like cell division, flagellum positioning, and chemotaxis. A prominent example of intracellular patterns are the oscillatory pole-to-pole…
In order to understand the nuclei which develop during the course of protein folding and unfolding, we examine phase segregation of a single heteropolymer chain which occurs in equilibrium. These segregated conformations are characterized…
In metallic nanoparticles, the cluster geometric structures control the particle's electronic band structure, polarizability, and catalytic properties. Analyzing the structural properties is a complex problem; the structure of an assembled…
The structural evolution of a nano-powder by repeated dispersion and settling can lead to characteristic fractal substructures. This is shown by numerical simulations of a two-dimensional model agglomerate of adhesive rigid particles. The…