相关论文: On morphological and functional complexity of prot…
Accurate prediction of binding free energies is critical to streamlining the drug development and protein design process. With the advent of GPU acceleration, absolute alchemical methods, which simulate the removal of ligand electrostatics…
The effects of particle roughness and short-ranged non-central forces on colloidal gels are studied using computer simulations in which particles experience a sinusoidal variation in energy as they rotate. The number of minima $n$ and…
The self-assembly of particles into organized structures is a key feature of living organisms and a major engineering challenge. While it may proceed through the binding of perfectly matched, puzzle-pieces-like particles, many other…
We introduce a formulation for normal mode analyses of globular proteins that significantly improves on an earlier, 1-parameter formulation (M. Tirion, PRL 77, 1905 (1996)) that characterized the slow modes associated with protein data bank…
Soft gels, formed via the self-assembly of particulate organic materials, exhibit intricate multi-scale structures that provides them with flexibility and resilience when subjected to external stresses. This work combines molecular…
How to measure the complexity of a finite set of vectors embedded in a multidimensional space? This is a non-trivial question which can be approached in many different ways. Here we suggest a set of data complexity measures using universal…
This work explores the complexity and nonlinearity of seven different colloidal suspensions-Au, ferrofluid, TiO2}, ZnO, g-C3N4, MXene, and PEDOT:PSS-when electrically stimulated with fractal, chaotic, and random binary signals. The recorded…
Amino acids are essential to all life. However, our understanding of some aspects of their intrinsic structure, molecular chemistry, and electronic structure is still limited. In particular the nature of amino acids in their crystalline…
Protein function frequently involves conformational changes with large amplitude on timescales which are difficult and computationally expensive to access using molecular dynamics. In this paper, we report on the combination of three…
Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or…
The use of beta-solenoid proteins as functionalizable, nanoscale, self-assembling molecular building blocks may have many applications, including templating the growth of wires or higher-dimensional structures. By understanding their…
Understanding complex biological macromolecules, especially proteins, is vital for grasping their diverse chemical functions with direct impact in biology and pharmacology. While techniques like X-ray crystallography and cryo-electron…
Recent studies classify the topology of proteins by analysing the distribution of their projections using knotoids. The approximation of this distribution depends on the number of projection directions that are sampled. Here we investigate…
Dispersed colloidal particles within a suspension can aggregate and spontaneously self-organize into a robust, percolating structure known as a gel. These network-like structures are prevalent in nature and play a critical role in many…
Polymers can be modeled as open polygonal paths and their closure generates knots. Knotted proteins detection is currently achieved via high-throughput methods based on a common framework insensitive to the handedness of knots. Here we…
In 1999 Wright and Dyson highlighted the fact that large sections of the proteome of all organisms are comprised of protein sequences that lack globular folded structures under physiological conditions. Since then the biophysics community…
Ligands entering a protein binding pocket essentially compete with water molecules for binding to the protein. Hence, the location and thermodynamic properties of water molecules in protein structures have gained increased attention in the…
We introduce a pipeline for representing a protein, or protein complex, as the union of signed distance functions (SDFs) by representing each atom as a sphere with the appropriate radius. While this idea has been used previously as a way to…
The Protein Data Bank (PDB) contains the atomic structures of over 105 biomolecules with better than 2.8A resolution. The listing of the identities and coordinates of the atoms comprising each macromolecule permits an analysis of the…
Proteins are the fundamental macromolecules that play diverse and crucial roles in all living matter and have tremendous implications in healthcare, manufacturing, and biotechnology. Their functions are largely determined by the sequences…