Related papers: First-principles design of nanomachines
The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry…
Proteins are linear chain molecules that play a central role in life and health. Protein native state folds are modular assemblies of space-filling building blocks of {\alpha}-helices, \{beta}-sheets and tight turns. Here we deduce the…
We study nanomachines whose relevant (effective) degrees of freedom f >> 1 but smaller than f of proteins. In these machines, both the entropic and the quantum effects over the whole system play the essential roles in producing nontrivial…
DNA nanoparticles with three-fold coordination have been observed to self-assemble in experiment into a network equivalent to the hexagonal (6.6.6) tiling, and a network equivalent to the 4.8.8 Archimedean tiling. Both networks are built…
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…
Obtaining microscopic structure-property relationships for grain boundaries are challenging because of the complex atomic structures that underlie their behavior. This has led to recent efforts to obtain these relationships with machine…
The theory of elastic rods can be used to describe certain geometric and topological properties of the DNA molecules. A similar effective field theory approach was previously suggested to describe the conformations and dynamics of proteins.…
A practical, biologically motivated case of protein complexes (immunoglobulin G and FcRII receptors) moving on the surface of mastcells, that are common parts of an immunological system, is investigated. Proteins are considered as…
Materials that behave like machines, e.g. functional materials that are able to change shape in response to external stimuli (Bhattacharya and James, 2005), often do so by exploiting phase transitions. Shape memory materials and the tail…
Self-organizing nanocheckerboards have been experimentally fabricated in Mn-based spinels, but have not yet been explained with first principles. Using density-functional-theory, we explain the phase diagram of the…
Functional nanoparticles (NPs) have gained significant attention as a promising application in various fields, including sensor, smart coating, drug delivery, and more. Here, we propose a novel mechanism assisted by machine-learning…
Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…
Functionalization of nanoparticles or colloids is increasingly being used to develop customizable "atoms". Functionalization by attaching single strands of DNA allows for direct control of the binding between nanoparticles, since…
Molecular chaperones are machines that consume copious amount of ATP to drive misfolded proteins or RNA to fold into functionally competent native states. Because the folding landscapes of biomolecules with complex native state topology are…
Proteins are the common constituents of all living cells. They are molecular machines that interact with each other as well as with other cell products and carry out a dizzying array of functions with distinction. These interactions follow…
An In Silico model to relate the properties of proteins to the structure, sequence, function and evolutionary history of proteins is shown. The derived ideal sequences for amino acid residues in proteins can then be considered as attractors…
Exploring the use of individual molecules as active components in electronic devices has been at the forefront of nanoelectronics research in recent years. Compared to semiconductor microelectronics, modeling transport in single-molecule…
Proteins are macromolecules that mediate a significant fraction of the cellular processes that underlie life. An important task in bioengineering is designing proteins with specific 3D structures and chemical properties which enable…
One-dimensional NMR spectroscopy is one of the most widely used techniques for the characterization of organic compounds and natural products. For molecules with up to 36 non-hydrogen atoms, the number of possible structures has been…
A neuron transforms its input into output spikes, and this transformation is the basic unit of computation in the nervous system. The spiking response of the neuron to a complex, time-varying input can be predicted from the detailed…