相关论文: Hamiltonian Dynamics of Saturated Elongation in Am…

In the study of amyloid fiber formation, the fiber length distribution plays a central role. From this microscopic distribution, all macroscopic statistical quantities, like the fiber number concentration P(t) and mass concentration M(t),…

Protein molecules often self-assemble by means of non-covalent physical bonds to form extended filaments, such as amyloids, F-actin, intermediate filaments, and many others. The kinetics of filament growth is limited by the disassembly…

A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…

We consider a relativistic extended object described by a reparametrization invariant local action that depends on the extrinsic curvature of the worldvolume swept out by the object as it evolves. We provide a Hamiltonian formulation of the…

The Hamiltonian dynamics of chains of nonlinearly coupled particles is numerically investigated in two and three dimensions. Simple, off-lattice homopolymer models are used to represent the interparticle potentials. Time averages of…

The phase behavior of colloidal particles embedded in a binary fluid is influenced by wetting layers surrounding each particle. The free energy of the fluid film depends on its morphology, i.e., on size, shape and connectivity. Under rather…

A new method is proposed for integrating the equations of motion of an elastic filament. In the standard finite-difference and finite-element formulations the continuum equations of motion are discretized in space and time, but it is then…

We consider the dynamics of a rigid filament in a motor protein assay under external loading. The motor proteins are modeled as active harmonic linkers with tail ends immobilized on a substrate. Their heads attach to the filament…

In this work we developed a theoretical model to describe the polymerization of very long macromolecules with simultaneous precipitation. As a reference system for our model we consider UHMWPE polymerization process, via homogeneous…

In this work, we underline the importance of the molecular weight of hyaluronic acid on the elongational properties of concentrated emulsions. The filament formation properties, e.g. the stringiness, of an emulsion is a key determinant of a…

We consider the Regge-Teitelboim model for a relativistic extended object embedded in a fixed background Minkowski spacetime, in which the dynamics is determined by an action proportional to the integral of the scalar curvature of the…

Mechanical strength of amyloid beta fibrils has been known to be correlated with neuronal cell death. Here, we resorted to steered molecular dynamics (SMD) simulations to mechanically stretch a single S-shape amyloid beta Abeta11-42…

Many proteins have the potential to aggregate into amyloid fibrils, which are associated with a wide range of human disorders including Alzheimer's and Parkinson's disease. In contrast to that of folded proteins, the thermodynamic stability…

Lattice computations in the Hamiltonian formulation have so far mainly focused on staggered fermions. In these proceedings, we study Wilson fermions in the Hamiltonian formulation and propose a new method to determine the resulting mass…

We develop a computational method to learn a molecular Hamiltonian matrix from matrix-valued time series of the electron density. As we demonstrate for three small molecules, the resulting Hamiltonians can be used for electron density…

Self-assembly of proteins is a biological phenomenon which gives rise to spontaneous formation of amyloid fibrils or polymers. The starting point of this phase, called nucleation exhibits an important variability among replicated…

Water activity and its relationship with interactions stabilising lamellar stacks of mixed lipid bilayers in their fluid state are investigated by means of osmotic pressure measurements coupled with small-angle x-ray scattering. The…

We study an intricate mechanism of pattern formation in globally coupled heterogeneous oscillatory media. In anodic electrochemical etching of silicon, the electrode surface splits into two amplitude-phase regions, while all oscillators…

A plausible consequence of rugged energy landscapes of biomolecules is that functionally competent folded states may not be unique, as is generally assumed. Indeed, molecule-to-molecule variations in the dynamics of enzymes and ribozymes…

We carry out a theoretical study on the isotropic-nematic phase transition and phase separation in amyloid fibril solutions. Borrowing the thermodynamic model employed in the study of cylindrical micelles, we investigate the variations in…