Related papers: Molecular dynamics study of molecular mobility in …
Reversible bipolar nano-switches that can be set and read electronically in a solid-state two-terminal device are very promising for applications. We have performed molecular-dynamics simulations that mimic systems with oxygen vacancies…
We have adapted classical molecular dynamics to study the structural and dynamical properties of amorphous silica surfaces. Concerning the structure, the density profile exhibits oscillations perpendicularly to the surface as observed in…
We study the dynamics of quantum excitations inside macromolecules which can undergo conformational transitions. In the first part of the paper, we use the path integral formalism to rigorously derive a set of coupled equations of motion…
Biochars have been attracting renewed attention as economical and environmentally friendly carbon sequestration materials with a diverse range of applications. However, experimental developments may be limited by the lack of molecular-level…
The transport phenomena of Lennard-Jones molecules through a structural bottleneck driven by an external force are investigated by molecular dynamics simulations. We observe two distinct molecular flow regimes distinguished by a critical…
Mixtures of active and passive particles are ubiquitous at the microscale. Many essential microbial processes involve interactions with dead or immotile cells or passive crowders. When passive objects are immersed in active baths, their…
Our published and new experimental results by means of deuteron NMR spectroscopy in studies of molecular mobility in confinement are summarized and annalysed. Conclusions about limits of applicability of methods in disclosing several…
In the present paper we deal with nonlinear dynamics of microtubules (MTs). The structure and role of MTs in cells are explained. One model explaining MT dynamics is explained. Solutions of the crucial nonlinear differential equation depend…
We propose a two-dimensional model for the organization of stabilized microtubules driven by molecular motors in an unconfined geometry. In this model two kinds of dynamics are competing. The first one is purely diffusive, with an…
A simple phenomenological model for describing the conformational dynamics of biological macromolecules via the nonlinearity-induced instabilities is proposed. It is shown that the interaction between charges and bending degrees of freedom…
Molecular dynamics (MD) is a widely-used tool for simulating the molecular and materials properties. It is a common wisdom that molecular dynamics simulations should obey physical laws and, hence, lots of effort is put into ensuring that…
Molecular dynamics refers to the computer simulation of a material at the atomic level. An open problem in numerical analysis is to explain the apparent reliability of molecular dynamics simulations. The difficulty is that individual…
Many natural and industrial processes rely on constrained transport, such as proteins moving through cells, particles confined in nanocomposite materials or gels, individuals in highly dense collec- tives and vehicular traffic conditions.…
The traffic of molecular motors which interact through mutual exclusion is studied theoretically for half-open tube-like compartments. These half-open tubes mimic the shapes of axons. The mutual exclusion leads to traffic jams or density…
Both molecular mechanical and quantum mechanical calculations play an important role in describing the behavior and structure of molecules. In this work, we compare for the same peptide systems the results obtained from folding molecular…
The rotating-wave approximation to light-matter interactions is widely used in the quantum electrodynamics Hamiltonian; however, its validity has long been a matter of debate. In this article, we explore the impact of the rotating-wave…
A tutorial introduction to the technique of Molecular Dynamics (MD) is given, and some characteristic examples of applications are described. The purpose and scope of these simulations and the relation to other simulation methods is…
The effect of laser fields on the electron transport through a molecular wire being weakly coupled to two leads is investigated. The molecular wire acts as a coherent quantum ratchet if the molecule is composed of periodically arranged,…
Inspired by biological molecular machines we explore the idea of an active quantum robot whose purpose is delaying decoherence. A conceptual model capable of partially protecting arbitrary logical qubit states against single physical qubit…
The applicability of computational and dynamical systems models to organisms is scrutinized, using examples from developmental biology and cognition. Developmental morphogenesis is dependent on the inherent material properties of developing…