Related papers: Single-molecule pulling: phenomenology and interpr…
The measurement of cellular traction forces on soft elastic substrates has become a standard tool for many labs working on mechanobiology. Here we review the basic principles and different variants of this approach. In general, the…
Single and collective cell migration are fundamental processes critical for physiological phenomena ranging from embryonic development and immune response to wound healing and cancer metastasis. To understand cell migration from a physical…
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly…
Molecular dynamics simulations are used to study the behavior of closely-fitting spherical and ellipsoidal particles moving through a fluid-filled cylinder at nanometer scales. The particle, the cylinder wall and the fluid solvent are all…
Single-chain nanoparticles (SCNPs) are a new class of macromolecular objects, synthesized through purely intramolecular cross-linking of single polymer chains. We use a multi-scale hydrodynamics simulation approach to study, for the first…
We extend the generating function technique for calculation of single molecule photon emission statistics [Y. Zheng and F. L. H. Brown, Phys. Rev. Lett., 90,238305 (2003)] to systems governed by multi-level quantum dynamics. This opens up…
In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…
Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the…
We investigate the thermopower of single molecules weakly coupled to metallic leads. We model the molecule in terms of the relevant electronic orbitals coupled to phonons corresponding to both internal vibrations and to oscillations of the…
The self-assembly of molecules at surfaces can be caused by a range of physical mechanisms. Assembly can be driven by intermolecular forces, or molecule-surface forces, or both; it can result in structures that are in equilibrium or that…
The mechanical stretching of single poly-proteins is an emerging tool for the study of protein (un)folding, chemical catalysis and polymer physics at the single molecule level. The observed processes i.e unfolding or reduction events, are…
Progress on researches in the field of molecules at cold and ultracold temperatures is reported in this review. It covers extensively the experimental methods to produce, detect and characterize cold and ultracold molecules including…
We describe a simple automated method to extract and quantify transient heterogeneous dynamical changes from large datasets generated in single molecule/particle tracking experiments. Based on wavelet transform, the method transforms raw…
A protein undergoes conformational dynamics with multiple time scales, which results in fluctuating enzyme activities. Recent studies in single molecule enzymology have observe this "age-old" dynamic disorder phenomenon directly. However,…
Quantifying the outcomes of cells collisions is a crucial step in building the foundations of a kinetic theory of living matter. Here, we develop a mechanical theory of such collisions by first representing individual cells as extended…
The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their…
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…
Single molecules are nanoscale thermodynamic systems with few degrees of freedom. Thus, the knowledge of their entropy can reveal the presence of microscopic electron transfer dynamics, that are difficult to observe otherwise. Here, we…
General discrete one-dimensional stochastic models to describe the transport of single molecules along coupled parallel lattices with period $N$ are developed. Theoretical analysis that allows to calculate explicitly the steady-state…
Human physiology and pathology arise from the coordinated interactions of diverse single cells. However, analyzing single cells has been limited by the low sensitivity and throughput of analytical methods. DNA sequencing has recently made…