Related papers: Dynamic polarizability of macromolecules for singl…
Spectroscopic techniques are essential tools for determining the structure of molecules. Different spectroscopic techniques, such as Nuclear magnetic resonance (NMR), Infrared spectroscopy, and Mass Spectrometry, provide insight into the…
An important aspect of astrophysical MHD turbulence research is developing diagnostics to connect simulations with the observable universe. Turbulent systems are by definition structurally complex in all fluid variables (density, velocity,…
The analysis of live-cell single-molecule imaging experiments can reveal valuable information about the heterogeneity of transport processes and interactions between cell components. These characteristics are seen as motion changes in the…
Simulating the dynamics of ions near polarizable nanoparticles (NPs) using coarse-grained models is extremely challenging due to the need to solve the Poisson equation at every simulation timestep. Recently, a molecular dynamics (MD) method…
Living organisms are molecular systems with self-sustained dynamics via energy conversion through molecular cooperation, resulting in highly complex macroscopic behaviors. Construction of such autonomous macroscopic dynamics at a molecular…
Jamming is a phenomenon shared by a wide variety of systems, such as granular materials, foams, and glasses in their high density regime. This has motivated the development of a theoretical framework capable of explaining many of their…
This technical note introduces parametric dynamic causal modelling, a method for inferring slow changes in biophysical parameters that control fluctuations of fast neuronal states. The application domain we have in mind is inferring slow…
Microtubules are filament-shaped, polymeric proteins (~25 nm in diameter) involved in cellular structure and organization. We demonstrate the imaging of individual microtubules using a conventional bright-field microscope, without any…
The internal dynamics of macro-molecular systems is characterized by widely separated time scales, ranging from fraction of ps to ns. In ordinary molecular dynamics simulations, the elementary time step dt used to integrate the equation of…
We study dynamics of a probe molecule, driven by an external constant force in a liquid monolayer on top of solid surface. In terms of a microscopic, mean-field-type approach, we calculate the terminal velocity of the probe molecule. This…
We study the density-density response function of a collection of charged massive Dirac particles and present analytical expressions for the dynamical polarization function in one, two and three dimensions. The polarization function is then…
Single-beam super-resolution microscopy, also known as superlinear microscopy, exploits the nonlinear response of fluorescent probes in confocal microscopy. The technique requires no complex purpose-built system, light field modulation, or…
We present a pump-probe technique for monitoring ultrafast polarizability changes. In particular, we use it to measure the plasma density created at the temporal focus of a self-compressing higher-order pump soliton in gas-filled…
We consider an ensemble of diatomic molecules resonantly coupled to an optical cavity under strong coupling conditions at normal incidence. Photodissociation dynamics is examined via direct numerical integration of the coupled…
Dynamic properties of molecular motors that fuel their motion by actively interacting with underlying molecular tracks are studied theoretically via discrete-state stochastic ``burnt-bridge'' models. The transport of the particles is viewed…
Molecular dynamics simulations of a glass-forming model system are performed under application of a microrheological perturbation on a tagged particle. The trajectory of that particle is studied in its underlying potential energy landscape.…
We describe a method to compute photon-matter interaction and atomic dynamics with X-ray lasers using a hybrid code based on classical molecular dynamics and collisional-radiative calculations. The forces between the atoms are dynamically…
Confocal microscopy of fluorescent labeled particles has been used to study the dynamical and structural properties of colloidal and granular matter in real space. Localization algorithms allow for a fully automatized determination of the…
In polydisperse systems, describing the structure and any structural order parameter (SOP) is not trivial as it varies with the number of species we use to describe the system, M . Depending on the degree of polydispersity, there is an…
Biophysicists and structural biologists increasingly acknowledge the role played by the mechanical properties of macromolecules as a critical element in many biological processes. This change has been brought about, in part, by the advent…