Related papers: First-principles design of nanomachines
We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we…
Carbon nanotubes are modeled as point particle configurations in the framework of Molecular Mechanics, where interactions are described by means of short range attractive-repulsive potentials. The identification of local energy minimizers…
Self-assembled patterns obtained from a drying nanosphere suspension are investigated by computer simulations and simple experiments. Motivated by the earlier experimental results of Sasaki and Hane and Schope, we confirm that more ordered…
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…
Machine learning has emerged as an invaluable tool in many research areas. In the present work, we harness this power to predict highly accurate molecular infrared spectra with unprecedented computational efficiency. To account for…
The protein design problem involves finding polypeptide sequences folding into a given threedimensional structure. Its rigorous algorithmic solution is computationally demanding, involving a nested search in sequence and structure spaces.…
Recently, we presented a framework for understanding protein structure based on the idea that simple constructs of holding hands or touching of objects can be used to rationalize the common characteristics of globular proteins. We developed…
Single-chain nanoparticles (SCNPs) are a new class of macromolecular objects, synthesized through purely intramolecular cross-linking of single polymer chains. We use a multi-scale hydrodynamics simulation approach to study, for the first…
We demonstrate a machine learning approach designed to extract hidden chemistry/physics to facilitate new materials discovery. In particular, we propose a novel method for learning latent knowledge from material structure data in which…
Graphs are central to the chemical sciences, providing a natural language to describe molecules, proteins, reactions, and industrial processes. They capture interactions and structures that underpin materials, biology, and medicine. This…
Fundamental questions about the role of the quaternary structures are addressed using a statistical mechanics off-lattice model of a dimer protein. The model, in spite of its simplicity, captures key features of the monomer-monomer…
Molecular spiders are synthetic molecular motors based on DNA nanotechnology. While natural molecular motors have evolved towards very high efficiency, it remains a major challenge to develop efficient designs for man-made molecular motors.…
The presence of nanoparticles in a diblock copolymer leads to changes in the morphology and properties of the matrix and can produce highly organized hybrid materials. The resulting material properties depend not only on the polymer…
In soft matter science, it is often the goal to design new materials with targeted properties. These materials can be used in many applications, each requiring specific features to be optimized for maximum fitness. The use of self-assembly…
We introduce a scheme for molecular simulations, the Deep Potential Molecular Dynamics (DeePMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data.…
The functionality of proteins is related to their structure in the native state. Protein structures are made up of emergent building blocks of helices and almost planar sheets. A simple coarse-grained geometrical model of a flexible tube…
The anisotropic feature of charge transfer reactions in realistic proteins cannot be ignored, due to the highly complex chemical structure of bio-molecules. In this work, we have performed the first large-scale quantitative assessment of…
A microscopic model is proposed for the interactions between sickle hemoglobin molecules based on information from the protein data bank. A Monte Carlo simulation of a simplified two patch model is carried out, with the goal of…
A fascinating and open question challenging biochemistry, physics and even geometry is the presence of highly regular motifs such as alpha-helices in the folded state of biopolymers and proteins. Stimulating explanations ranging from…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…