Related papers: Topological potentials guiding protein self-assemb…

Topology optimization of microstructures plays a critical role in optimizing functional performance across diverse engineering applications. While metamaterials with enhanced mechanical properties -- such as hyperelasticity, energy…

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…

Self-assembly kinetics is usually described by approaches which assume that the shape of the aggregates has a definite form (e.g., spherical, cylindrical, cubic, etc), however that is unlikely to be the case in many finite-sized…

The functioning of machines typically requires a concerted action of their parts. This requirement also holds for molecular motors that drive vital cellular processes and imposes constraints on their conformational changes as well as the…

Hierarchically structured natural materials possess functionalities unattainable to the same components organized or mixed in simpler ways. For instance, the bones and teeth of mammals are far stronger and more durable than the mineral…

Most approaches for designing self-assembled materials focus on the thermodynamic stability of a target structure or crystal polymorph. Yet in practice, the outcome of a self-assembly process is often controlled by kinetic pathways. Here we…

We introduce a method of exploring potential energy contours in complex dynamical systems based on potentiostatic kinematics wherein the systems are evolved with minimal changes to their potential energy. We construct a simple iterative…

Cytoskeletal filaments are capable of self-assembly in the absence of externally supplied chemical energy, but the rapid turnover rates essential for their biological function require a constant flux of ATP or GTP hydrolysis. The same is…

Thanks to a constant energy input, active matter can self-assemble into phases with complex architectures and functionalities such as living clusters that dynamically form, reshape and break-up, which are forbidden in equilibrium materials…

The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…

Complex colloidal cluster morphologies are desirable for the fabrication of advanced materials, such as photonic crystals and meta-materials, and can be formed through evaporation-driven packing. By coupling lattice Boltzmann and discrete…

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…

A topology optimization method is presented for the design of periodic microstructured materials with prescribed homogenized nonlinear constitutive properties over finite strain ranges. The mechanical model assumes linear elastic isotropic…

Comparing mathematical models offers a means to evaluate competing scientific theories. However, exact methods of model calibration are not applicable to many probabilistic models which simulate high-dimensional spatio-temporal data.…

The precise sequence of aminoacids plays a central role in the tertiary structure of proteins and their functional properties. The Hydrophobic-Polar lattice models have provided valuable insights regarding the energy landscape. We…

Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…

One of the challenging issues in additive manufacturing (AM) oriented topology optimization is how to design structures that are self-supportive in a manufacture process without introducing additional supporting materials. In the present…

Living systems exhibit complex yet organized behavior on multiple spatiotemporal scales. To investigate the nature of multiscale coordination in living systems, one needs a meaningful and systematic way to quantify the complex dynamics, a…

In equilibrium self-assembly, microscopic building blocks spontaneously self-organize into stable structures as dictated by their interaction potentials, which limits the accessible structural features to those that correspond to global…

Due to its non-crystalline nature, the glassy state has remained one the most exciting scientific challenges. To study such materials, Molecular Dynamics (MD) simulations have been extensively used because they provide a direct view into…