相关论文: Influence of pH and sequence in peptide aggregatio…
We performed "weighted ensemble" path-sampling simulations of adenylate kinase, using several semi-atomistic protein models. Our study investigated both the biophysics of conformational transitions as well as the possibility of increasing…
The density of a protein molecule is a key property within a variety of experimental techniques. We present a computational method for determining protein mass density that explicitly incorporates hydration effects. Our approach uses…
Recent years have seen tremendous developments in the use of machine learning models to link amino acid sequence, structure and function of folded proteins. These methods are, however, rarely applicable to the wide range of proteins and…
We develop a theory of aggregation using statistical mechanical methods. An example of a complicated aggregation system with several levels of structures is peptide/protein self-assembly. The problem of protein aggregation is important for…
Electronically-active organic molecules have demonstrated great promise as novel soft materials for energy harvesting and transport. Self-assembled nanoaggregates formed from $\pi$-conjugated oligopeptides composed of an aromatic core…
Results on the production of $\pi^{\pm}$, $\textrm{K}^{\pm}$, $\textrm{p}(\bar{\textrm{p}})$, $\Lambda(\bar{\Lambda})$, $\Xi^{-} \left(\bar{\Xi}^{+}\right)$ and $\Omega^{-} \left(\bar{\Omega}^{+}\right)$ at midrapidity (${|y|<0.5}$) as a…
Nanoparticle (NP)-protein complexes exhibit the correct identity of NP in biological media. Therefore, protein-NP interactions should be closely explored to understand and to modulate the nature of NPs in medical implementations. This…
The presence of interparticle cohesion can drastically change the behavior of granular materials. For instance, powders are challenging to handle, and one can make a sandcastle using wet grains. In this study, we report experimental results…
Finite-temperature properties of graphene monolayers under tensile stress have been studied by path-integral molecular dynamics (PIMD) simulations. This method allows one to consider the quantization of vibrational modes in these…
``Seeding'' is the addition of preformed fibrils to a solution of monomeric protein to accelerate its aggregation into new fibrils. It is a versatile and widely-used tool for scientists studying protein aggregation kinetics, as it enables…
Peptides and proteins exhibit a common tendency to assemble into highly ordered fibrillar aggregates, whose formation proceeds in a nucleation-dependent manner that is often preceded by the formation of disordered oligomeric assemblies.…
An accurate map of intracellular organelle pH is crucial for comprehending cellular metabolism and organellar functions. However, a unified intracellular pH spectrum using a single probe is still lack. Here, we developed a novel quantum…
Recent experiments have identified peptides with adhesion affinity for GaAs and Si surfaces. Here we use all-atom Monte Carlo (MC) simulations with implicit solvent to investigate the behavior in aqueous solution of four such peptides, all…
We describe a simple ansatz to approximate the low temperature behavior of proteins and peptides by a mean-field-like model which is analytically solvable. For a small peptide some thermodynamic quantities are calculated and compared with…
A theory for sequence dependent liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs) in the study of biomolecular condensates is formulated by extending the random phase approximation (RPA) and field-theoretic…
We discuss variance reduced simulations for an individual-based model of chemotaxis of bacteria with internal dynamics. The variance reduction is achieved via a coupling of this model with a simpler process in which the internal dynamics…
Nuclear quantum effects (NQEs) remain a major challenge for molecular simulations, as rigorous treatment requires imaginary-time path-integral methods with heavy computational overhead. Neglecting NQEs leads to systematic errors in…
The effect of melting in planetary mantles plays a key role in their thermo-chemical evolution. Because of the laterally heterogeneous nature of melting, 3D numerical simulations are in principle necessary prohibiting us from exploring wide…
In the protein sequence space, natural proteins form clusters of families which are characterized by their unique native folds whereas the great majority of random polypeptides are neither clustered nor foldable to unique structures. Since…
We consider the problem of heterogeneous nucleation and growth. The system is described by a phase field model in which the temperature is included through thermal noise. We show that this phase field approach is suitable to describe…