Related papers: Quantitative evaluation of methods to analyze moti…
The turn of the millennium has seen a growing interest in the study of live cells by infrared (IR) spectroscopy, driven by the versatility, wealth of molecular information, and potential for high-throughput screening of the technique.…
We study dynamics of a probe particle, which performs biased diffusive motion in a one-dimensional adsorbed monolayer of mobile hard-core particles undergoing continuous exchanges with a vapor phase. In terms of a mean-field-type approach,…
Our knowledge of how individual cells self-organize to form complex multicellular systems is being revolutionized by a data outburst, coming from high-throughput experimental breakthroughs such as single-cell RNA sequencing and spatially…
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…
Intracellular transport of DNA carriers is a fundamental step of gene delivery. We present here a theoretical approach to study generically a single virus or DNA particle trafficking in a cell cytoplasm. Cellular trafficking has been…
Water molecules confined between biological membranes exhibit a distinctive non-Gaussian displacement distribution, far different from bulk water. Here, we introduce a new transport equation for water molecules in the intermembrane space,…
We show how one can measure the signal from slow jumps of a single molecule between metastable positions using a setup where the molecule is fixed to one lead, and one of the coupling strengths is controlled externally. Such a measurement…
Understanding molecular state evolution is central to many disciplines, including molecular dynamics, precision measurement, and molecule-based quantum technology. Details of the evolution are obscured when observing a statistical ensemble…
All-atom simulations can provide molecular-level insights into the dynamics of gas-phase, condensed-phase and surface processes. One important requirement is a sufficiently realistic and detailed description of the underlying intermolecular…
Dusty plasma medium turns out to be an ideal system for studying the strongly coupled behavior of matter. The large size and slow response make their dynamics suitable to be captured through simple diagnostic tools. Furthermore, as the…
We use molecular dynamic simulations to investigate the relation between the presence of packing defects in a glass-former and the spontaneous cooperative motions called dynamic heterogeneity. For that purpose we use a simple diatomic…
Motor-driven intracellular transport of organelles, vesicles, and other molecular cargo is a highly collective process. An individual cargo is often pulled by a team of transport motors, with numbers ranging from only a few to several…
An open problem in numerical analysis is to explain why molecular dynamics works. The difficulty is that numerical trajectories are only accurate for very short times, whereas the simulations are performed over long time intervals. It is…
This dissertation explores the application of machine learning in molecular biology, focusing on gene expression regulation and cellular behavior at the single-cell level. Using modern neural networks, the research addresses key challenges…
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…
Distinguishing active from passive dynamics is a fundamental challenge in understanding the motion of living cells and other active matter systems. Here, we introduce a framework that combines physical modeling, analytical theory, and…
Inhibiting a signalling pathway concerns controlling the cellular processes of a cancer cell's viability, cell division, and death. Assay protocols created to see if the molecular structures of the drugs being tested have the desired…
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…
The dynamics of single cell migration on flat surfaces is usually modeled by a Langevin-like problem consisting of ballistic motion for short periods and random walk. for long periods. Conversely, recent studies have revealed a previously…
Exchange of biochemical substances is essential way in establishing communication between bacterial cells. It is noticeable that all phases of the process are heavily influenced by perturbations of either internal or external parameters.…