Related papers: Unfolding Large Biomolecules
Many biological processes can be thought of as the result of an underlying dynamics in which the system repeatedly undergoes distinct and abortive trajectories with the dynamical process only ending when some specific process, purpose,…
Ion traps, which were first introduced in the late 1950s and early 1960s, have established themselves as indispensable tools in many areas of physics, chemistry and technology. This chapter gives a brief survey of the operating principles…
Growing and studying large Coulomb crystals, composed of tens to hundreds of thousands of ions, in linear quadrupole ion traps presents new challenges for trap implementation. We consider several trap designs, first comparing the total…
Collective motion of self-propelled organisms or synthetic particles often termed active fluid has attracted enormous attention in broad scientific community because of it fundamentally non-equilibrium nature. Energy input and interactions…
Biomolecular condensates play a crucial role in the spatial organization of living matter. These membrane-less organelles, resulting from liquid-liquid phase separation, operate far from thermodynamic equilibrium, with their size and…
Phase separation drives the formation of biomolecular condensates in cells, which comprise many components and sometimes possess multiple phases. The equilibrium physics of phase separation is well understood, but many components in…
Cooling of ions or other charged particles in electromagnetic traps is an essential tool to achieve control over their degrees of freedom on the quantum level. For many objects, there is no viable route for direct cooling, such as an…
We develop the theory describing the quantum coupled dynamics of the center-of-mass motion of a nanoparticle and an ensemble of ions co-trapped in a dual-frequency linear Paul trap. We first derive analytical expressions for the motional…
The nonequilibrium activity taking place in a living cell can be monitored with a tracer embedded in the medium. While microrheology experiments based on optical manipulation of such probes have become increasingly standard, we put forward…
Mechanical oscillators based on levitated particles are promising candidates for sensitive detectors and platforms for testing fundamental physics. The targeted quality factors for such oscillators correspond to extremely low damping rates…
Multipole radiofrequency ion traps are a highly versatile tool to study molecular ions and their interactions in a well-controllable environment. In particular the cryogenic 22-pole ion trap configuration is used to study ion-molecule…
Biomolecules carry out very specialized tasks inside the cell where energies involved are few tens of k_BT, small enough for thermal fluctuations to be relevant in many biomolecular processes. In this paper I discuss a few concepts and…
Life is characterized by a myriad of complex dynamic processes allowing organisms to grow, reproduce, and evolve. Physical approaches for describing systems out of thermodynamic equilibrium have been increasingly applied to living systems,…
The motion of a eukaryotic cell presents a variety of interesting and challenging problems from both a modeling and a computational perspective. The processes span many spatial scales (from molecular to tissue) as well as disparate time…
Biomolecular condensates are essential for cellular organization and result from phase separation in systems far from thermodynamic equilibrium. Among various models, chemically active droplets play a significant role, consisting of…
Flagellar-driven locomotion plays a critical role in bacterial attachment and colonization of surfaces, contributing to the risks of contamination and infection. Tremendous attempts to uncover the underlying principles governing bacterial…
We experimentally demonstrate optical dipole trapping of a cloud of cold atoms by means of a dynamically coupled mode of a high-finesse cavity. We show that the trap requires a collective action of the atoms, i.e. a single atom would not be…
A scheme for fast, compact, and controllable acceleration of heavy particles in vacuum is proposed, in which two counterpropagating lasers with variable frequencies drive a beat-wave structure with variable phase velocity, thus allowing for…
The Brownian dynamics of a single microorganism coupled by chemotaxis to a diffusing concentration field which is secreted by the microorganism itself is studied by computer simulations in spatial dimensions $d=1,2,3$. Both cases of a…
A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…