Related papers: Colloidal particle motion as a diagnostic of DNA c…
Revealing possible long-living coherence in ultrafast processes allows detecting genuine quantum mechanical effects in molecules. To investigate such effects from a quantum chemistry perspective, we have developed a method for simulating…
Topological data analysis (TDA) is a versatile tool that can be used to extract scientific knowledge from complex pattern formation processes. However, the physics correspondence between the features obtained from TDA and pattern dynamics…
Miniaturized, self-propelled locomotors use chemo-mechanical transduction mechanisms to convert fuel in the environment to autonomous motion. Recent experimental and theoretical studies demonstrate that these autonomous engines can…
The motion of a particle under the influence of a dynamical disorder is described by the DLD model. One motivation is to understand the motion of an electron inside a metal; Another is to understand quantal Brownian motion. The overview is…
This paper studies the particle motion when the tune is in the stable region close to the edge of linear sum resonance stopband. Results are found for the tune and the beta functions. Results are also found for the two solutions of the…
We present a quantitative, multi-scale coarse-grained model of DNA coated colloids. The parameters of this model are transferable and are solely based on experimental data. As a test case, we focus on nano-sized colloids carrying…
The importance of torsion vibration in the transmission of life information is indicated. The localization of quantum torsion state is proved. Following these analyses a formalism on the quantum theory of conformation-electron system is…
We study multifractal properties in time evolution of a single particle subject to repeated measurements. For quantum systems, we consider circuit models consisting of local unitary gates and local projective measurements. For classical…
The tethered-particle method is a single-molecule technique that has been used to explore the dynamics of a variety of macromolecules of biological interest. We give a theoretical analysis of the particle motions in such experiments. Our…
Molecular search phenomena are observed in a variety of chemical and biological systems. During the search the participating particles frequently move in complex inhomogeneous environments with random transitions between different dynamic…
Photoelectron momentum distributions (PMDs) from atoms and molecules undergo qualitative changes as laser parameters are varied. We present a model to interpret the shape of the PMDs. The electron's motion is guided by a fictitious particle…
The TATA-box Binding Protein (TBP) is required by all three eukaryotic RNA polymerases for the initiation of transcription from most promoters. TBP recognizes, binds to, and bends promoter sequences called ``TATA-boxes'' in the DNA. We…
Particle tracking is commonly used to study time-dependent behavior in many different types of physical and chemical systems involving constituents that span many length scales, including atoms, molecules, nanoparticles, granular particles,…
A single semiflexible polymer chain folds into a toroidal object under poor solvent conditions. In this study, we examined the morphological change in such a toroidal state as a function of the width and stiffness of the chain together with…
A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…
We study the motion of a charged particle under the action of a magnetic field with cylindrical symmetry. In particular we consider magnetic fields with constant direction and with magnitude depending on the distance $r$ from the symmetry…
Here we demonstrate a synthetic micro-engine, based on long-range controlled movement of colloidal particles, which is induced by a local catalytic reaction. The directed motion at long timescales was achieved by placing specially designed…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…
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…
Cloaking is a method of making obstacles undetectable. Here we cloak unit cells of a magnetic pattern squeezed into an otherwise periodic pattern from a magnetically driven colloidal flow. We apply a time-periodic external magnetic field…