Related papers: Molecular dynamics study of molecular mobility in …
The exploring and understanding the electronic properties of molecules connected to metallic leads is a vital part of nanoscience if molecule is to have a future. This thesis documents a study for various families of organic and…
We use colloidal suspensions encapsulated in emulsion droplets to model confined glass-forming liquids with tunable boundary mobility. We show dynamics in these idealized systems are governed by physical interactions with the boundary.…
The decay of field-free rotational dynamics is experimentally studied in two complementary methods: laser-induced molecular alignment and terahertz-field-induced molecular orientation. Comparison between the decay rates of different…
Transport phenomena in out-of-equilibrium systems is immensely important in a myriad of applications in biology, engineering and physics. Complex environments, such as the cytoplasm or porous media, can substantially affect the transport…
The dynamic behavior of a partially wetting polymer droplet driven over a nanostructured interface is studied using molecular dynamics simulations. We consider the bead-spring model to represent a polymeric liquid that partially wets a…
This paper presents a novel approach to the description and understanding of two-dimensional binary cellular automata with the Moore neighborhood that preserve the number of active cells. Such dynamical systems are known to successfully…
Molecular dynamics simulation is used to investigate the crystallization of a classical two-dimensional electron system, in which electrons interact with the Coulomb repulsion. From the positional and the orientational correlation…
-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…
All-atom and coarse-grained molecular dynamics are two widely used computational tools to study the conformational states of proteins. Yet, these two simulation methods suffer from the fact that without access to supercomputing resources,…
A geometrical model which captures the main ingredients governing atom-diatom collinear chemical reactions is proposed. This model is neither near-integrable nor hyperbolic, yet it is amenable to analysis using a combination of the recently…
We study the dynamical response of a circularly-driven rigid body, focusing on the description of intrinsic rotational behavior (reverse rotations). The model system we address is integrable but nontrivial, allowing for qualitative and…
We present a realistic model of the fragile glass former orthoterphenyl and the results of extensive molecular dynamics simulations in which we investigated its basic static and dynamic properties. In this model the internal molecular…
Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and…
We explore the quantum dynamics of heteronuclear atomic collisions in waveguides and demonstrate the existence of a novel mechanism for the resonant formation of polar molecules. The molecular formation probabilities can be tuned by…
Molecular machines transduce free energy between different forms throughout all living organisms. While truly machines in their own right, unlike their macroscopic counterparts molecular machines are characterized by stochastic…
Many biological functions are executed by molecular machines, which consume energy and convert it into mechanical work. Biological machines have evolved to transport cargo, facilitate folding of proteins and RNA, remodel chromatin and…
Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations have been developed to simulate molecular systems, where an explicit description of changes in the electronic structure is necessary. However, QM/MM MD…
A general framework for performing event-driven simulations of systems with semi-flexible or rigid bodies interacting under impulsive torques and forces is outlined. Two different approaches are presented. In the first, the dynamics and…
Cells are complex structures which require considerable amounts of organization via transport of large intracellular cargo. While passive diffusion is often sufficiently fast for the transport of smaller cargo, active transport is necessary…
We present a systematic understanding of the rotational structure of a long-range (vibrationally highly-excited) diatomic molecule. For example, we show that depending on a quantum defect, the least-bound vibrational state of a diatomic…