Related papers: Dynamic polarizability of macromolecules for singl…
Molecular motor proteins form the basis of cellular dynamics. Recently, notable efforts have led to the creation of their DNA-based mimics, which can carry out complex nanoscale motion. However, such functional analogues have not yet been…
An ensemble of directed macromolecules on a lattice is considered, where the constituting molecules are chosen as a random sequence of N different types. The same type of molecules experiences a hard-core (exclusion) interaction. We study…
Polaritonic chemistry offers the possibility of modifying molecular properties and even influencing chemical reactivity through strong coupling between vibrational transitions and confined light modes in optical cavities. Despite…
The formation and regulation of macromolecular complexes provides the backbone of most cellular processes, including gene regulation and signal transduction. The inherent complexity of assembling macromolecular structures makes current…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
Cellular signaling is essential in information processing and decision making. Therefore, a variety of experimental approaches have been developed to study signaling on bulk and single-cell level. Single-cell measurements of signaling…
Optical fluorescence imaging is capable of measuring both the spatial and rotational dynamics of single molecules. However, unavoidable measurement noise will result in inaccurate estimates of rotational dynamics, causing a molecule to…
As the ultimate miniaturization of semiconductor devices approaches, it is imperative that the effects of single dopants be clarified. Beyond providing insight into functions and limitations of conventional devices, such information enables…
The Monte Carlo simulation of the dynamics of complex molecules produces trajectories with a large number of different configurations to sample configuration space. It is expected that these configurations can be classified into a small…
Recent technological advances in cutting-edge ultrasensitive fluorescence microscopy have allowed single-molecule imaging experiments in living cells across all three domains of life to become commonplace. Single-molecule live-cell data is…
We study, both theoretically and experimentally, the dynamical polarizability $\alpha(\omega)$ of $\textrm{Rb}_2$ molecules in the rovibrational ground state of $\mathrm{a}^3\Sigma_u^+$. Taking all relevant excited molecular bound states…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
The question on the dominant driving mechanism (displacive or order-disorder) at each structural phase transition of KNbO3 is investigated by means of molecular dynamics simulations. To this purpose, we first develop a shell model by…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
We use molecular dynamic to simulate the directional growth of binary mixtures. our results compare very well with analitical and experimental results. This opens up the possibility to probe growth situations which are difficult to reach…
We describe a new generation of algorithms capable of mapping the structure and conformations of macromolecules and their complexes from large ensembles of heterogeneous snapshots, and demonstrate the feasibility of determining both…
Membrane pores are implicated in several critical functions, including cell fusion and the transport of signaling molecules for intercellular communication. However, these structural features are often difficult to probe directly. Droplet…
We present a modelling framework for the dynamics of cells structured by the concentration of a micromolecule they contain. We derive general equations for the evolution of the cell population and of the extra-cellular concentration of the…
Using a realistic flexible molecule model of the fragile glass former orthoterphenyl, we calculate via molecular dynamics simulation the collective dynamic structure factor, recently measured in this system by Inelastic X-ray Scattering.…
The intermittent transition between slow growth and rapid shrinkage in polymeric assemblies is termed dynamic instability, a feature observed in a variety of biochemically distinct assemblies including microtubules, actin and their…