相关论文: Hamiltonian Dynamics of Saturated Elongation in Am…
Amyloid fibers are aggregates of proteins. They are built out of a peptide called $\beta$--amyloid (A$\beta$) containing between 41 and 43 residues, produced by the action of an enzyme which cleaves a much larger protein known as the…
The presence of magnetic fields in many astrophysical objects is due to dynamo action, whereby a part of the kinetic energy is converted into magnetic energy. A turbulent dynamo that produces magnetic field structures on the same scale as…
It is well-known that the formation of amyloid fiber may cause invertible damage to cells, while the underlying mechanism has not been fully uncovered. In this paper, we construct a mathematical model, consisting of infinite ODEs in the…
We use Brownian dynamics simulations and theory to study the over-damped spatiotemporal dynamics and pattern formation in a fluid-permeated array of equally spaced, active, elastic filaments that are pinned at one end and free at the other.…
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…
During the application of mass-action equation models to the study of amyloid fiber formation, time-consuming numerical calculations constitute a major bottleneck when no analytical solution is available. To conquer this difficulty, here an…
This paper presents a theoretical model for studying the dynamics of ordering in alloys which exhibit modulated phases. The model is different from the standard time-dependent Ginzburg-Landau description of the evolution of a non-conserved…
Fiber reinforced materials (FRMs) can be modeled as bi-phasic materials, where different constitutive behaviors are associated with different phases. The numerical study of FRMs through a full geometrical resolution of the two phases is…
We derive in this note a high-order corrector estimate for the homogenization of a microscopic semi-linear elliptic system posed in perforated domains. The major challenges are the presence of nonlinear volume and surface reaction rates.…
Point defects critically influence the properties of materials and devices, yet density functional theory (DFT) remains computationally demanding for defect supercell calculations. Machine learning interatomic potentials (MLIPs) offer high…
The aggregation of amyloid-forming peptides is a dynamic, complex process that underlies their diverse biological activities, from physiological functions to disease-associated dysfunctions. While the structure of fibrillar end-products is…
We propose a kinetic model for the self-aggregation by amyloid proteins. By extending several well-known models for protein aggregation, the time evolution of aggregate concentrations containing $r$ proteins, denoted $c_r(t)$, can be…
Protein oligomers have been implicated as toxic agents in a wide range of amyloid-related diseases. Yet it has remained unsolved whether the oligomers are a necessary step in the formation of amyloid fibrils, or just a dangerous by-product.…
We systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics…
We analyse a generalisation of Z\"{o}ttl and Stark's model of active spherical particles [Phys. Rev. Lett. 108, 218104 (2012)] and prolate spheroidal particles [Eur. Phys. J. E 36(1), 4 (2013)] suspended in cylindrical Poiseuille flow, to…
Simulated annealing (SA) is a kind of relaxation method for finding equilibria of Hamiltonian systems. A set of evolution equations is solved with SA, which is derived from the original Hamiltonian system so that the energy of the system…
Protein amyloidosis is a cytopathological process characterized by the formation of highly beta-sheet-rich fibrils. How this process occurs and how to prevent/treat the associated diseases are not completely understood. Here, we carry out a…
Recent experimental studies have shown that amyloid fibril formed by aggregation of {\beta} peptide exhibits excellent mechanical properties comparable to other protein materials such as actin filaments and microtubules. These excellent…
We study the modular Hamiltonians of an interval for the massless Dirac fermion on the half-line. The most general boundary conditions ensuring the global energy conservation lead to consider two phases, where either the vector or the axial…
The aim of this work is to study fiber derivatives associated to Lagrangian and Hamiltonian functions describing the dynamics of a higher-order autonomous dynamical system. More precisely, given a function in $T^*T^{(k-1)}Q$, we find…