Related papers: Self-folding Self-replication
This study presents a theoretical model for a self-replicating mechanical system inspired by biological processes within living cells and supported by computer simulations. The model decomposes self-replication into core components, each of…
At the cutting edge of materials science, matter is designed to self-organize into structures that perform a wide range of functions. The past two decades have witnessed major innovations in the versatility of building blocks, ranging from…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
A self-replicator is usually understood to be an object of definite form that promotes the conversion of materials in its environment into a nearly identical copy of itself. The challenge of engineering novel, micro- or nano-scale…
We provide partial implementations of von Neumann's universal constructor and universal copier, starting out with three types of simple building blocks using minimal assumptions. Using the same principles, we also construct Turing machines.…
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…
Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…
The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…
Protein folding models have achieved groundbreaking results typically via a combination of integrating domain knowledge into the architectural blocks and training pipelines. Nonetheless, given the success of generative models across…
The design space for a self-assembled multicomponent objects ranges from a solution in which every building block is unique to one with the minimum number of distinct building blocks that unambiguously define the target structure. Using a…
Protein structures are a very special class among all possible structures. It was suggested that a ``designability principle'' plays a crucial role in nature's selection of protein sequences and structures. Here we provide a theoretical…
It has been argued that a central objective of nanotechnology is to make products inexpensively, and that self-replication is an effective approach to very low-cost manufacturing. The research presented here is intended to be a step towards…
The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction,…
We describe the results obtained from an improved model for protein folding. We find that a good agreement with the native structure of a 46 residue long, five-letter protein segment is obtained by carefully tuning the parameters of the…
We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We postulate a compatible solvent-mediated emergent pairwise…
In this work, we describe a self-replication-based mechanism for designing agents of increasing complexity. We demonstrate the validity of this approach by solving simple, standard evolutionary computation problems in simulation. In the…
Protein one-dimensional (1D) structures such as secondary structure and contact number provide intuitive pictures to understand how the native three-dimensional (3D) structure of a protein is encoded in the amino acid sequence. However, it…
Molecular robotics is challenging, so it seems best to keep it simple. We consider an abstract molecular robotics model based on simple folding instructions that execute asynchronously. Turning Machines are a simple 1D to 2D folding model,…
Can active forces be exploited to drive the consistent collapse of an active polymer into a folded structure? In this paper we introduce and perform numerical simulations of a simple model of active colloidal folders, and show that a…
We investigate the crumpling of a sheet as it is repeatedly crushed onto itself by rolling it into a cylinder and twisting it axially while allowing the end-to-end length to evolve freely. As deduced from its plastic deformations, the sheet…