Related papers: Non-exponential relaxation and hierarchically cons…
We study a class of nonlocal, energy-driven dynamical models that govern the motion of closed, embedded curves from both an energetic and dynamical perspective. Our energetic results provide a variety of ways to understand physically…
The process of structural relaxation in disordered solids subjected to repeated tension-compression loading is studied using molecular dynamics simulations. The binary glass is prepared by rapid cooling well below the glass transition…
Controlled quantum systems such as ultracold atoms can provide powerful platforms to study non-equilibrium dynamics of closed many-body quantum systems, especially since a complete theoretical description is generally challenging. In this…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
The characterization of finite-time thermodynamic processes is of crucial importance for extending equilibrium thermodynamics to nonequilibrium thermodynamics. The central issue is to quantify responses of thermodynamic variables and…
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…
In Part I of this contribution, a systematic coarse-grained description of the dynamics of a weakly-bending semiflexible polymer was developed. Here, we discuss analytical solutions of the established deterministic partial…
Cochlea displays complex and highly nonlinear behavior in response to wide-ranging auditory stimuli. While there have been many recent advancements in the modeling of cochlear dynamics, it remains unclear what mathematical structures…
We propose a discrete model to determine the metabolic scaling exponent based on Fibonacci growth patterns and discrete biological development phases. In contrast to continuous fractal models such as the West-Brown-Enquist (WBE) theory, the…
The Hubbard model is a prototype for strongly correlated electrons in condensed matter, for molecules and fermions or bosons in optical lattices. While the equilibrium properties of these systems have been studied in detail, the excitation…
Current mathematical frameworks for predicting the flux state and macromolecular composition of the cell do not rely on thermodynamic constraints to determine the spontaneous direction of reactions. These predictions may be biologically…
Phase separation has emerged as an essential concept for the spatial organization inside biological cells. However, despite the clear relevance to virtually all physiological functions, we understand surprisingly little about what phases…
Confinement of dynamical fields can be attributed to the absence of corresponding asymptotic states. Thermodynamical properties of such system are more appropriately formulated in terms of collective excitations of these fields, if they…
We simulate a relaxation process of non-brownian particles in a sheared viscous medium; the small shear strain is initially applied to a system, which then undergoes relaxation. The relaxation time and the correlation length are estimated…
We systematically investigated the impact of boundary confinement on the shear-thickening rheology of dense granular suspensions. Under highly confined conditions, dense suspensions were found to exhibit size-dependent or even rarely…
A theory for kinetic arrest in isotropic systems of repulsive, radially-interacting particles is presented that predicts exponents for the scaling of various macroscopic quantities near the rigidity transition that are in agreement with…
Relaxation dynamics, as a key to understand glass formation and glassy properties, remains an elusive and challenging issue in condensed matter physics. In this work, in situ high-pressure synchrotron high-energy x-ray photon correlation…
Sampling from flat energy or density distributions has proven useful in equilibrating complex systems with large energy barriers. Several thermostats and barostats are presented to sample these flat distributions by molecular dynamics.…
We present a thermodynamically consistent mesoscopic model of protein adsorption at liquid-solid interfaces. First describing the equilibrium state under varying protein concentration of the solution and binding conditions, we predict a…
We study the dynamics of non-aligning, non-interacting self-propelled particles confined to a box in two dimensions. In the strong confinement limit, when the persistence length of the active particles is much larger than the size of the…