Related papers: How Cations Change Peptide Structure
It is expected that atomic vacancies or nanometric cavities reduce the number of chemical bonds of nearby atoms and hence the strength of a voided solid. However, the hardness of a porous specimen does not always follow this simple picture…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
Nanoparticles can influence the properties of polymer materials by a variety of mechanisms. With fullerene, carbon nanotube, and clay or graphene sheet nanocomposites in mind, we investigate how particle shape influences the melt shear…
We study statistical properties of interacting protein-like surfaces and predict two strong, related effects: (i) statistically enhanced self-attraction of proteins; (ii) statistically enhanced attraction of proteins with similar…
We investigate vibration modes and their Raman activity of single-walled carbon nanotubes that are bent within their intrinsic elastic limits. By implementing novel boundary conditions for density-functional based tight-binding, and using…
We investigate the effect of lattice disorder and local correlation effects in finite and periodic silicene structures caused by carbon doping using first-principles calculations. For both finite and periodic silicene structures, the…
Proteins are minimally frustrated polymers. However, for realistic protein models non-native interactions must be taken into account. In this paper we analyze the effect of non-native interactions on the folding rate and on the folding free…
Density functional methods have been used to calculate the electronic properties of aligned smalldiameter single-walled carbon nanotubes under hydrostatic pressures. Abrupt pressure induced semiconductor-metal and metal-semiconductor…
Experimental investigations of the biosynthesis of a number of proteins have pointed out that part of the native structure can be acquired already during translation. We carried out a comprehensive statistical analysis of some average…
Although wettability is a macroscopic manifestation of molecular-level forces, such as van der Waals (vdW) forces, the impact of nanoconfinement on material properties in reduced film thickness remains unexplored in predicting film…
Grate and co-workers at Pacific Northwest National Laboratory recently developed high information content triazine-based sequence-defined polymers that are robust by not having hydrolyzable bonds and can encode structure and functionality…
The high rates of multi-parton interactions at the LHC can provide a unique opportunity to study the multi-parton structure of the hadron. To this purpose high energy collisions of protons with nuclei are particularly suitable. The rates of…
The conformations available to polypeptides are determined by the interatomic forces acting on the peptide units, whereby backbone torsion angles are restricted as described by the Ramachandran plot. Although typical proteins are composed…
The protein-protein interactions (PPIs) are crucial for understanding the majority of cellular processes. PPIs play important role in gene transcription regulation, cellular signaling, molecular basis of immune response and more. Moreover,…
We have examined the electronic structure evolution in transition metal dichalcogenides MX$_2$, where M=Mo,W and X=S,Se and Te. These are generally referred to as van der Waals heterostructures on the one hand, yet one has band gap changes…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…
The coil-globule transition of hetero-polymer chains is studied here. By means of extensive Molecular Dynamics simulations, we show that the transition is directly linked to the complexity of the chain, which depends on the number of…
Despite the potential paradigm breaking capability of microcavities to control chemical processes, the extent to which photonic devices change properties of molecular materials is still unclear, in part due to challenges in modeling hybrid…