Related papers: Statistical physics and mesoscopic modeling to int…
When very small particles are suspended in a fluid in motion, they tend to follow the flow. How such tracer particles are mixed, transported, and dispersed by turbulent flow has been successfully described by statistical models. Heavy…
We consider an active, stochastic microscopic model of particles suspended in a fluid and show that the coarse-grained description of this model renders odd viscoelasticity. The particles are odd dumbbells, each featuring a robotic device…
Short DNA linkers are increasingly being exploited for driving specific self-assembly of Brownian objects. DNA-functionalised colloids can assemble into ordered or amorphous materials with tailored morphology. Recently, the same approach…
Modelling quantum devices is to find a model according to quantum theory that can explain the result of experiments in a quantum device. We find that usually we cannot correctly identify the model describing the actual physics of the device…
Years ago Edwards proposed a thermodynamic description of dense granular matter, in which the grains (the `atoms' of the system) interact with inelastic forces. The approach is intriguing but is not justified from first principles, and…
We provide a numerical study of the macroscopic model of [3] derived from an agent-based model for a system of particles interacting through a dynamical network of links. Assuming that the network remodelling process is very fast, the…
Precise modelling of a signal in processes with multiple observables, exhibiting a complex dependency on the underlying parameters, is often a difficult and challenging task. Predicting the results of experimental measurements in…
Optical microscopy provides rich spatio-temporal information characterizing in vivo molecular motion. However, effective forces and other parameters used to summarize molecular motion change over time in live cells due to latent state…
Current physics models used to interpret experimental measurements of particle beams require either simplifying assumptions to be made in order to ensure analytical tractability, or black box optimization methods to perform model based…
The theory of elastic rods can be used to describe certain geometric and topological properties of the DNA molecules. A similar effective field theory approach was previously suggested to describe the conformations and dynamics of proteins.…
Form a pure mathematical point of view, common functional forms representing different physical phenomena can be defined. For example, rates of chemical reactions, diffusion and heat transfer are all governed by exponential-type…
Nucleic acids have been regarded as stiff polymers with long-range flexibility and generally modeled using elastic rod models of polymer physics. Notwithstanding, investigations carried out over the past few years on single fragments of…
Single cell responses are shaped by the geometry of signaling kinetic trajectories carved in a multidimensional space spanned by signaling protein abundances. It is however challenging to assay large number (>3) of signaling species in…
Recently, much attention has been focused on the replicability of scientific results, causing scientists, statisticians, and journal editors to examine closely their methodologies and publishing criteria. Experimental particle physicists…
Self-propelling active matter relies on the conversion of energy from the undirected, nanoscopic scale to directed, macroscopic motion. One of the challenges in the design of synthetic active matter lies in the control of dynamic states, or…
Discrete simulation methods are efficient tools to investigate the complex behaviors of complex fluids made of either dry granular materials or dilute suspensions. By contrast, materials made of soft and/or concentrated units (emulsions,…
Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. While there is a large body of experimental work which allows us to accurately separate different topoisomers of a molecule, a full…
Three coarse-grained models of the double-stranded DNA are proposed and compared in the context of mechanical manipulation such as twisting and various schemes of stretching. The models differ in the number of effective beads (between two…
Many cell functions are accomplished thanks to intracellular transport mechanisms of macromolecules along filaments. Molecular motors such as dynein or kinesin are proteins playing a primary role in these processes. The behavior of such…
Mass spectrometry is a widely used method to study molecules and processes in medicine, life sciences, chemistry, catalysis, and industrial product quality control, among many other applications. One of the main features of some mass…