相关论文: Molecular Dynamics Simulation of Amyloid Beta Dime…
We perform numerical simulations of isolated, partially active polymers, driven out-of-equilibrium by a fraction of their monomers. We show that, if the active beads are all gathered in a contiguous block, the position of the section along…
Protein aggregation into insoluble amyloid-like fibrils is implicated in a wide range of diseases and understanding its nucleation process is a key for mechanistic insights and advancing therapeutics. The electronic charge of the…
Atomistic molecular dynamics simulations have reached a degree of maturity that makes it possible to investigate the lipid polymorphism of model bilayers over a wide range of temperatures. However if both the fluid $L_{\alpha}$ and tilted…
The determination of the folding mechanisms of proteins is critical to understand the topological change that can propagate Alzheimer and Creutzfeld-Jakobs diseases, among others. The computational community has paid considerable attention…
We propose a mathematical model for the onset and progression of Alzheimer's disease based on transport and diffusion equations. We treat brain neurons as a continuous medium and structure them by their degree of malfunctioning. Three…
The author gave the sharp asymptotic behavior of the free energy of $1+1$ dimensional directed polymers in random environment(DPRE) as the inverse temperature $\beta\to 0$ under the assumption that random environment satisfies a certain…
We describe a computational model for studying the complexity of self-assembled structures with active molecular components. Our model captures notions of growth and movement ubiquitous in biological systems. The model is inspired by…
Molecular dynamics simulations are used to study the phase behavior of a single linear multiblock copolymer with blocks of A- and B-type monomers under poor solvent conditions, varying the block length $N$, number of blocks $n$, and the…
Alzheimer's disease (AD) is a neurodegenerative disease characterized by dementia and memory loss in the elderly population. The amyloid-$\beta$ peptide (A$\beta$ 1-42) is one of the main pathogenic factors in AD and is known to cause…
Segments with the amino acid sequence EKAYLRT appear in natural occurring proteins both in $\alpha$-helices and $\beta$-sheets. For this reason, we have use this peptide to study how secondary structure formation in proteins depends on the…
We propose a simple microscopic model of molecular dynamics simulation to study orientational glass in three dimensions. We present simulation results for mixtures of mildly anisotropic particles and spherical impurities. We realize fcc…
We consider a bilayer setup with two parallel planes of cold fermionic polar molecules when the dipole moments are oriented perpendicular to the planes. The binding energy of two-body states with one polar molecule in each layer is…
Above a critical concentration a wide variety of peptides and proteins self-assemble into amyloid fibrils which entangle to form percolating networks called hydrogels. Such hydrogels have important applications as biomaterials and in…
The discovery of polymers with targeted properties is challenged by the vast chemical design space and the limited availability of consistent, high-quality data across multiple properties. In this work, an integrated polymer informatics…
A question of considerable interest to cell membrane biology is whether phase segregated domains across an asymmetric bilayer are strongly correlated with each other and whether phase segregation in one leaflet can induce segregation in the…
By using molecular dynamics simulation, formation mechanisms of amorphous carbon in particular sp${}^3$ rich structure was researched. The problem that reactive empirical bond order potential cannot represent amorphous carbon properly was…
Using exhaustive Monte Carlo simulations we study the kinetics and mechanism of fibril formation using lattice models as a function of temperature and the number of chains. While these models are, at best, caricatures of peptides, we show…
Zinc is found saturated in the deposited Amyloid-beta (AB) peptide plaques in brains of patients subjected to Alzheimer disease (AD). Zinc binding to AB promotes aggregations, including the toxic soluble AB species. Up to now, only the…
Recent studies have shown that one-dimensional driven systems can exhibit phase separation even if the dynamics is governed by local rules. The ABC model, which comprises three particle species that diffuse asymmetrically around a ring,…
Theoretical approaches are formulated to investigate the molecular mobility under various cooling rates of amorphous drugs. We describe the structural relaxation of a tagged molecule as a coupled process of cage-scale dynamics and…