Related papers: Short-time dynamics of polypeptides
Polymer chains undergoing a continuous adsorption-desorption transition are studied through extensive computer simulations. A three-dimensional self-avoiding walk lattice model of a polymer chain grafted onto a surface has been treated for…
Proteins are linear chain molecules that play a central role in life and health. Protein native state folds are modular assemblies of space-filling building blocks of {\alpha}-helices, \{beta}-sheets and tight turns. Here we deduce the…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
We investigate the dynamics of nanoparticles in semidilute polymer solutions when the nanoparticles are comparably sized to the polymer coils using explicit- and implicit-solvent simulation methods. The nanoparticle dynamics are…
We inquire how structure emerges during the process of protein folding. For this we scrutinise col- lective many-atom motions during all-atom molecular dynamics simulations. We introduce, develop and employ various topological techniques,…
Arguments are presented that the reaction products of central high energy nuclear collisions up to collider energies can rigorously be interpreted in terms of a continuous decoupling mechanism based on continuous equations of motion. The…
By simulating the first order globule-crystal transition of a flexible homopolymer chain, both by collision dynamics and Monte Carlo with non-kinetic moves, we show that the effective and the thermodynamic transition temperatures are…
It is emphasized that the collective dynamics associated with color confinement is dominating over a point-like mechanism related to a scattering of the proton constituents at the currently available values of the momentum transferred in…
Weak interactions form the core basis of a vast number of biological processes, in particular, those involving intrinsically disordered proteins. Here, we establish a new technique capable of probing these weak interactions between…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely…
An introductory review to short-time critical dynamics is given. From the scaling relation valid already in the early stage of the evolution of a system at or near the critical point, one derives power law behaviour for various quantities.…
A framework is presented for understanding the common character of proteins. Proteins are linear chain molecules. However, the simple model of a polymer viewed as spheres tethered together does not account for many of the observed…
We examine the elastic model of short circular DNA. We obtain analytic expressions for configurations, elastic energy, twist and linking number of our solutions. We find the onset of the plectonemic transition. We suggest ways to use our…
Transition metal complexes for photochemical applications often feature a high density of electron-vibrational states characterized by nonadiabatic and spin-orbit couplings. Overall, the dynamics after photoexcitation is shaped by rapid…
The protein dynamical transition is investigated as a function of protein structure using terahertz time domain spectroscopy (THz-TDS). Measurements performed for native state and denatured hen egg white lysozyme (HEWL) show that protein…
We study conformational transitions of simple coarse-grained models for protein-like heteropolymers on the simple cubic lattice and off-lattice, respectively, by means of multicanonical sampling algorithms. The effective hydrophobic/polar…
We review the physical properties of macromolecular networks, consisting of semiflexible polymers such as actin. We start by giving a theoretical analysis of the conformational statistics and mechanical response of single filaments.…
We study the equilibrium properties of a flexible homopolymer where consecutive monomers are represented by impenetrable hard spheres that are tangent to each other, and non-consecutive monomers interact via a square-well potential. To this…
Proteins are fundamental components of biological systems and can be represented through various modalities, including sequences, structures, and textual descriptions. Despite the advances in deep learning and scientific large language…